Microorganisms having increased lipid productivity

ABSTRACT

The present invention provides mutant microorganism that have higher lipid productivity than the wild type microorganisms from which they are derived while biomass at levels that are within approximately 50% of wild type biomass productivities under nitrogen replete conditions. Particular mutants produce at least twice as much FAME lipid as wild type while producing at least 75% of the biomass produced by wild type cells under nitrogen replete conditions. Also provided are methods of producing lipid using the mutant strains.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 15/210,845 filed Jul. 15, 2016, now pending; which claims the benefit under 35 USC § 119(e) to U.S. Application Ser. No. 62/318,161 filed Apr. 4, 2016 and to U.S. Application Ser. No. 62/192,510 filed Jul. 14, 2015. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The material in the accompanying sequence listing is hereby incorporated by reference into the application. The accompanying sequence listing text file, named SGI1920-3_ST25, was created on Feb. 5, 2019 and is 229 KB in size. The file can be accessed using Microsoft Word on a computer that uses Window OS.

BACKGROUND OF THE INVENTION

The invention relates to mutant microorganisms, such as algae and heterokonts, having increased lipid productivity and their use in producing lipids.

Many microorganisms such as algae, labyrinthulomycetes (“chytrids”), and oleaginous yeast induce lipid biosynthesis in response to nutrient stress, for example nitrogen starvation. Under conditions of nitrogen depletion, such microorganisms redirect compound biosynthesis from protein to storage lipids, typically triacylglyceride lipids (“TAG”). Because nitrogen depletion simultaneously decreases cell growth, optimal lipid biosynthesis is limited to a relatively short window before the cells become too metabolically impaired to maintain high levels of production.

Microalgal-derived biodiesel has long been considered a viable alternative to conventional petroleum-based fuels. However, despite decades of biological research, depriving strains of essential macronutrients such as nitrogen, phosphorous, or silicon, to obtain high lipid yields—conditions under which growth of the host microorganism is compromised—remains the modus operandi. Little progress has been made in engineering algal strains to accumulate lipid while maintaining growth as there is only nascent understanding of the regulation of metabolism underlying lipid accumulation (Courchesne et al. (2009) J. Biotechnol. 141:31-41; Goncalves et al. (2016) Plant Biotechnol. J. doi:1111/12523)

Various attempts to improve lipid productivity by increasing lipid biosynthesis during nutrient replete growth have focused on manipulating genes encoding enzymes for nitrogen assimilation or lipid metabolism as well as genes encoding polypeptides involved in lipid storage. For example, US2014/0162330 discloses a Phaeodactylum tricornutum strain in which the nitrate reductase (NR) gene has been attenuated by RNAi-based knockdown; Trentacoste et al. ((2013) Proc. Natl. Acad. Sci. USA 110: 19748-19753) disclose diatoms transformed with an RNAi construct targeting the Thaps3_264297 gene predicted to be involved in lipid catabolism; and WO2011127118 discloses transformation of Chlamydomonas with genes encoding oleosins (lipid storage protein) as well as with genes encoding diacylglycerol transferase (DGAT) genes. Although in each case increased lipid production was asserted based on microscopy or staining with lipophilic dyes, no quantitation of lipid by the manipulated cells was provided, nor was the relationship between biomass and lipid productivities over time determined.

WO 2011/097261 and US 2012/0322157 report that a gene denoted “SN03” encoding an arrestin protein has a role in increasing lipid production under nutrient replete conditions when overexpressed in Chlamydomonas. However, overexpression of the SNO3 gene was observed to result in the appearance of unidentified polar lipids, which were not quantified, and did not result in an increase in triglycerides (TAG). Another polypeptide identified as potentially regulating stress-induced lipid biosynthesis has been described by Boyle et al. ((2012) J. Biol. Chem. 287:15811-15825). Knockout of the NRR1 gene in Chlamydomonas encoding a “SQUAMOUSA” domain polypeptide resulted in a reduction of lipid biosynthesis with respect to wild type cells under nitrogen depletion; however, no mutants were obtained demonstrating increased lipid production. US 2010/0255550 recommends the overexpression of putative transcription factors (“TF1, TF2, TF3, TF4, and TF5”) in algal cells to increase lipid production, but no mutants having enhanced lipid production are disclosed.

Daboussi et al. 2014 (Nature Comm. 5:3881) report that disruption of the UGPase gene in Phaeodactylum triconornutum, which is believed to provide precursors to laminarin (storage carbohydrate) synthesis, results in increased lipid accumulation. However, no biochemical data was shown to indicate that laminarin content was affected and lipid and biomass productivities were not reported. Similarly, several groups have reported increases in lipid accumulation in Chlamydomonas starchless mutants (Wang et al. 2009 Eukaryotic Cell 8:1856-1868; Li et al. 2010 Metab Eng. 12:387-391) but successive reports that actually measured lipid productivity concluded that these strains were impaired in growth when grown in phototrophic conditions (Siaut et al. 2011 BMC Biotechnol. 11:7; Davey et al. 2014 Eukaryot Cell 13:392-400). These reports concluded that the highest lipid productivities (measured as TAG per liter per day) were actually achieved by the wild-type parental strain.

SUMMARY OF THE INVENTION

Algal mutants having elevated levels of constitutive lipid production are provided herein. As demonstrated in the examples, analysis of early transcriptional profiles of Nannochloropsis gaditana to N-deprivation revealed a novel negative regulator of lipid biosynthesis ZnCys-2845, a transcription factor of the fungal Zn(II)2Cys6 gene family. Using Cas9-mediated mutagenesis and RNAi technology, attenuated ZnCys strains were produced that were capable of partitioning approximately 45% of their total carbon content to lipids and of sustaining growth in a continuous growth system, resulting in a doubling of lipid productivity.

A first aspect of the invention is a mutant microorganism that produces at least 25% more lipid than is produced by a control microorganism while producing not less than 45% of the biomass produced by the control microorganism cultured under the same conditions, in which the culture conditions support production of biomass by the control microorganism. For example, a mutant microorganism as provided herein can produce at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100% more lipid than is produced by a control microorganism cultured under the same conditions as the mutant microorganism, which can be batch, semi-continuous, or continuous culture conditions, and in various embodiments are culture conditions in which the control microorganism accumulates biomass. The control microorganism can be, in some examples, a wild type microorganism, i.e., a wild type microorganism from which the mutant microorganism is directly or indirectly derived. The mutant microorganism can produce, in various embodiments, at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the control microorganism produces biomass, for example, produces biomass over the course of the culture or on a daily basis, under the culture conditions in which the mutant produces more lipid. In various examples a mutant microorganism as provided herein produces at least 50% of the biomass and at least 130%, at least 150%, at least 140%, at least 155%, at least 160%, at least 170%, at least 175%, at least 180%, at least 185%, at least 190%, at least 195%, at least 200%, at least 210%, or at least 215% of the amount of lipid produced by a wild type microorganism cultured under the same conditions, under which the wild type microorganism accumulates biomass. For example, the culture conditions can be nitrogen-replete with respect to the control or wild type microorganism.

A mutant microorganism as provided herein can produce at least 25% more FAME lipids than a control or wild type microorganism while producing at least 45% or at least about 50% as much biomass as the control or wild type microorganism over a culture period of at least three days, at least five days, at least seven days, at least eight days, at least ten days, at least twelve days, at least fifteen days, at least twenty days, at least thirty days, or at least sixty days. For example, the average daily FAME productivity can be at least 50% greater than that of a control or wild type microorganism while the average daily biomass (e.g., TOC) productivity can be at least 45% or at least about 50% that of the control or wild type microorganism over a culture period of at least three days, at least five days, at least seven days, at least ten days, at least twelve days, at least fifteen days, at least twenty days, at least thirty days, or at least sixty days. In particular examples, a mutant microorganism as provided herein can produce at least 50% more FAME lipids than a control or wild type microorganism while producing at least 60% as much biomass as the control microorganism over a culture period of at least seven days, at least eight days, or at least ten days where the daily amount of FAME produced by the mutant is not lower than the daily amount of FAME produced by the control or wild type microorganism on any day during the at least seven, at least eight, or at least ten day culture period. In further examples, the average daily FAME productivity of a mutant microorganism as provided herein can be at least 50% higher than the average daily FAME productivity of a control or wild type microorganism the average daily biomass productivity can be at least 50% of the average daily biomass productivity of the control microorganism over a culture period of at least seven days, at least eight days, or at least ten days where the daily amount of FAME produced by the mutant is not lower than the daily amount of FAME produced by the control or wild type microorganism on any day during the at least seven, at least eight, or at least ten day culture period.

For example, a mutant microorganism as provided herein can produce more FAME-derivatizable lipids (“FAME lipids” or “FAME”) than a control microorganism while producing not less than 45% of the biomass produced by the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the control microorganism produces biomass. A mutant microorganism as provided herein can have greater average daily FAME productivity than a control microorganism while exhibiting at least 45% of the average daily biomass productivity of the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the control microorganism produces biomass. In various examples, a mutant microorganism as provided herein produces at least 50% more FAME lipids while producing not less than about 50%, not less than about 60%, or not less than about 70% of the biomass produced by the control microorganism, when the mutant microorganism and control microorganism are cultured under the same culture conditions under which the culture of the control microorganism produces biomass, which can be nitrogen-replete culture conditions with respect to the control microorganism. The control microorganism in various embodiments can be a wild type microorganism, e.g., a wild type microorganism from which the mutant microorganism is directly or indirectly derived.

In some examples, the culture conditions under which the mutant produces more lipid than a control or wild type microorganism can be culture conditions in which the concentration of ammonium in the culture medium is less than about 2.5 mM, for example, less than about 2 mM, less than about 1.5 mM, less than about 1 mM, or less than or equal to about 0.5 mM. In some examples the culture medium can include no added ammonium or substantially no ammonium. In some examples, the culture medium can include no added source of reduced nitrogen for the microorganism, e.g., no added ammonium, urea, or amino acids that can be metabolized by the microorganism. The culture medium can in some examples include a nitrogen source such as, but not limited to, nitrate. Alternatively or in addition, the culture medium can include urea. In some examples, the culture medium is nutrient replete with respect to a wild type microorganism of the species from which the mutant microorganism is derived.

In various embodiments, the mutant microorganism can be a photosynthetic microorganism and the mutant microorganism can produce at least 25% more FAME lipids than a control microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control or wild type microorganism under photoautotrophic culture conditions. For example a mutant microorganism as provided herein can be an alga, such as a eukaryotic microalga, and can produce at least 25% more FAME lipids than a control or wild type microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control microorganism when both the control microorganism are cultured using inorganic carbon as substantially the sole source of carbon in the cultures. The control microorganism can be, for example, a wild type microorganism.

Culture conditions in which a mutant microorganism as provided herein can produce more FAME lipids than a control or wild type microorganism while producing at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% the amount of biomass as a control or wild type microorganism include any of batch, continuous, or semi-continuous culture conditions in which the control or wild type microorganism produces biomass. In various embodiments, a mutant microorganism as provided herein can produce at least 50% more FAME lipids than a control or wild type microorganism while producing at least 45%, at least about 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% as much biomass as the control or wild type microorganism over a culture period of at least three days, at least four days, at least five days, at least seven days, at least eight days, at least ten days, or at least twelve days. In some embodiments the average daily FAME productivity of a mutant microorganism is at least 50% more than that of a control or wild type microorganism while the average daily biomass productivity (e.g., TOC productivity) is at least 45%, at least about 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% as great as that of the control or wild type microorganism over the culture period, for example, over a culture period of at least three days, at least four days, at least five days, at least seven days, at least ten days, or at least twelve days.

In some examples, a mutant microorganism as provided herein can produce at least 50% more FAME lipids while producing at least about 75% of the amount of biomass produced by a wild type or control microorganism during a culture period of at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least thirteen days, for example, over a culture period of at least five, at least ten, at least fifteen, at least twenty, or at least thirty days where the mutant and control microorganism are cultured under the same conditions, under which both the mutant and control microorganisms produce biomass. For example, a mutant microorganism can demonstrate at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110%, or at least 120% higher FAME productivity and exhibit no more than a 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, or 1% decline in biomass (e.g., TOC) productivity with respect to a wild type or control microorganism cultured for at least five, at least six, at least seven, or at least eight days under conditions in which both the control and mutant microorganism cultures produce biomass. For example, the average daily FAME productivity of a mutant as provided herein can be at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110% more than that of a wild type or control microorganism and the average daily biomass (e.g., TOC) productivity can be at least about 50%, at least about 60%, at least about 70%, or at least about 80% of the average daily biomass productivity of the control microorganism under conditions in which both the control and mutant microorganism cultures are producing biomass. In various embodiments, the average daily FAME productivity of a mutant as provided herein can be at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, or at least 110% more than that of a wild type or control microorganism and the average daily biomass (e.g., TOC) productivity can be at least about 50%, at least about 60%, at least about 70%, or at least about 80% of the average daily biomass productivity of the control microorganism under conditions in which both the control and mutant microorganism cultures are producing biomass on a daily basis. In some examples, a mutant microorganism can produce at least 100% more or at least 120% more FAME lipids than a wild type or control microorganism while producing at least about 75% or at least about 80% of the biomass produced by a control type microorganism cultured under identical conditions which are nitrogen replete with respect to the control microorganism. In other examples a mutant microorganism can produce at least 75%, at least 80%, at least 85% more FAME lipids than a wild type or control microorganism while producing approximately as much biomass as is produced by a wild type microorganism cultured under identical conditions under which the wild type or control microorganism produces biomass, e.g., within 10% or within 5% of the amount of biomass produced by the control microorganism. In various examples, the average daily FAME productivity for at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, or at least thirteen days of culturing, for example, at least five, at least ten, at least fifteen, at least twenty, or at least thirty days of culturing can be at least 80% greater than the average daily FAME productivity of a wild type or control microorganism and the average daily biomass productivity can be substantially the same as that of a control or wild type microorganism cultured under identical conditions under which the wild type or control microorganism produces biomass, e.g., within 10%, within 5%, or within 2% of the biomass productivity of the control microorganism. The conditions in which a mutant microorganism produces at least 80% more FAME lipids than a wild type or control microorganism while producing at least as much biomass as produced by a wild type microorganism can be nutrient replete with respect to the wild type or control microorganism, and can be nitrogen replete with respect to the wild type or control microorganism. In various embodiments the mutant microorganism can be a photosynthetic microorganism, e.g., an alga, and the culture conditions under which the mutant alga has greater FAME productivity while producing at least 50% of the TOC as a control microorganism are photoautotrophic conditions.

A mutant microorganism as provided herein can have a FAME lipids (FAME) to total organic carbon (TOC) ratio at least 30% higher than the FAME/TOC ratio of the control microorganism under culture conditions in which the mutant microorganism produces at least 45% more FAME lipids and at least 50% as much biomass as the control microorganism. The FAME/TOC ratio of a mutant microorganism as provided herein can be, for example, at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, at least 150% higher, or at least 200% higher than the FAME/TOC ratio of a control or wild type microorganism cultured under identical conditions under which the control or wild type organism produces biomass, which may be nitrogen replete with respect to the wild type microorganism. In various embodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least 0.4, at least 0.5, at least 0.6, at least 0.7, or at least 0.8 while the mutant microorganism culture is accumulating TOC. For example, a mutant microorganism as provided herein can have at least 25% higher lipid productivity than a control microorganism while exhibiting not less than 45% or not less than about 50% of the average daily biomass productivity of the control microorganism, and can further have FAME lipids (FAME)/total organic carbon (TOC) ratios at least 30%, at least 50%, at least 70%, or at least 90% higher than the FAME/TOC ratio of a wild type microorganism, for at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fifteen, at least twenty, at least twenty-five, at least thirty, or at least sixty days of culturing, when the mutant microorganism and control microorganism are cultured under the same culture conditions in which both the mutant microorganism and control microorganism accumulate biomass, e.g., accumulate biomass on a daily basis. In various embodiments, the FAME/TOC ratio of the mutant is at least 0.3, at least 0.4, at least 0.5, at least 0.6, at least 0.7, at least 0.8, or between about 0.35 and 0.85, or between about 0.4 and about 0.8 while the mutant microorganism produces at least 50% of the TOC produced by the control microorganism over a period of at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fifteen, at least twenty, at least twenty-five, at least thirty, or at least sixty days of culturing, where the mutant and control microorganism are cultured under the same conditions and the mutant produces more lipid than the control microorganism, and both the mutant microorganism and the control microorganism produce biomass.

Thus, a further aspect of the invention is a mutant microorganism that exhibits a higher FAME/TOC ratio than is exhibited by a control microorganism when both the mutant microorganism and control microorganism are cultured under substantially identical conditions under which both the mutant microorganism and the control microorganism culture are accumulating TOC. In various examples, a mutant microorganism has a higher FAME/TOC ratio than is exhibited by a control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which both the control microorganism and the mutant microorganism produce biomass and the mutant microorganism culture produces at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or about or substantially the same amount of TOC as the wild type microorganism culture. The FAME/TOC ratio of a mutant microorganism as provided herein can be, for example, at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, or at least 150% higher than the FAME/TOC ratio of a control or wild type microorganism during a culture period in which the mutant microorganism produces at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or substantially the same amount of TOC as the wild type microorganism culture. For example, the average daily biomass productivity of a mutant microorganism can be at least about 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, that of a control or wild type microorganism culture, while having a FAME/TOC ratio at least 30% higher, at least 40% higher, at least 50% higher, at least 60% higher, at least 70% higher, at least 80% higher, at least 90% higher, at least 100% higher, at least 110% higher, at least 120% higher, at least 130% higher, at least 140% higher, or at least 150% higher than the FAME/TOC ratio of a control or wild type microorganism averaged over the same time period.

A mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 times the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. A mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 times the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass on a daily basis, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. In some embodiments the C:N ratio of a mutant as provided herein is between about 7 and between about 20, or between about 8 and about 17, or between about 10 and about 15, during the culture period in which mutant produces at least 50% more lipid that a control microorganism while producing at least 50% as much biomass as the control microorganism. A control microorganism in any of the embodiments or examples herein can be a wild type microorganism.

Alternatively or in addition, mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support biomass accumulation by the control microorganism (e.g., where the conditions support daily biomass accumulation by the control microorganism), can have reduced protein content when compared with a control microorganism. For example, a mutant microorganism as provided herein can have a decrease in protein content of at least 10%, at least 20%, at least 30%, at least 40%, at least 45%, or at least 50% with respect to a control microorganism. The mutant microorganism can partition at least 35%, at least 40%, or at least about 45% of its total carbon to lipid while producing at least 50% more lipid than a control microorganism under the same culture conditions in which the mutant microorganims produces at least 65%, at least 70%, at least 75%, at least 80% as much biomass as the control microorganism.

Further, a mutant microorganism such as any provided herein can in some embodiments have attenuated expression of a gene encoding a protein whose expression affects the expression of other genes, e.g., at least ten, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 additional genes. For example, a mutant as provided herein can have at least ten genes that are upregulated with respect to a wild type microorganism and at least ten genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (as disclosed herein) is displayed. A mutant as provided herein can have at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are upregulated with respect to a wild type microorganism and at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (e.g., greater lipid production with respect to the wild type microorganism) is expressed. In some embodiments, genes encoding polypeptides involved in protein synthesis can be upregulated in a mutant as provided herein, for example, genes encoding ribosomal polypeptides or other polypeptides that function in protein translation, including, without limitation, those belonging to gene ontology (GO) groups such as “translation”, “ribosome”, and/or “regulation of translation initiation”. Alternatively to or in combination with the upregulation of genes encoding polypeptides relating to protein synthesis, one or more genes encoding polypeptides involved in nitrogen assimilation such as one or more of a nitrite reductase, glutamine synthetase, ammonium transporter and/or an enzyme involved in molybdenum cofactor biosynthesis can be downregulated in a mutant as provided herein. Alternatively or in combination with any of the above, a mutant as provided herein can exhibit upregulation of one or more genes related to lipid biosynthesis including but not limited to desaturases, elongases, lipid droplet surface protein, and/or particular lipases, acyltransferases, and glyceraldehyde-3-phosphate dehydrogenases.

A mutant as described herein can be a mutant obtained by classical mutagenesis or can be a genetically engineered mutant. In various embodiments, a mutant microorganism as disclosed herein has been generated by introducing one or more genetic constructs (one or more nucleic acid molecules) into the microorganism. In some examples, one or more genetic constructs introduced into a microorganism are designed to attenuate expression of a native gene.

In various examples, mutants as disclosed herein can have attenuated expression of a fungal type Zn(2)Cys(6) transcription factor, i.e., a gene encoding a polypeptide that has a Zn(2)Cys(6) domain, e.g., has an amino acid sequence encoding a cd00067 “GAL4” domain or a “Zn_clus” domain belonging to pfam PF00172. For example, a mutant microorganism such as any disclosed herein having FAME production that is increased by at least 25% and biomass production that is reduced by no more than 50% with respect to a control microorganism for at least 3, at least 5, at least 7, at least 10, at least 12, at least 13, at least 15, at least 20, at least 25, or at least 30 days of culturing can have attenuated expression of a gene encoding a polypeptide that recruits to pfam PF00172. Alternatively or in addition, a mutant microorganism such as any disclosed herein having a FAME/TOC ratio that is at least 30% higher than the FAME/TOC ratio of a control microorganism under conditions in which the control microorganism is producing biomass can be a mutant microorganism that has attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., having an amino acid sequence encoding a domain belonging to pfam PF00172 or characterized as a cd00067 “GLA4” domain. In some examples, the Zn(2)Cys(6) domain can have at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3.

Thus, another aspect of the invention is mutant microorganism having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, wherein the mutant microorganism has increased partitioning of carbon to lipid with respect to a control microorganism that does not have attenuated expression of the gene encoding a polypeptide having a ZnCys domain. For example, a mutant microorganism as provided herein having attenuated expression of a polypeptide having a Zn(2)Cys(6) domain can have an increased FAME/TOC ratio with respect to a control cell when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism culture experiences an increase in TOC. In some examples, a mutant microorganism as provided herein can have a FAME/TOC ratio that is increased by at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, or at least 150% as compared to the FAME/TOC ratio of a control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism culture experiences an increase in TOC. Alternatively or in addition, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain can have increased production of FAME lipids with respect to a control microorganism while demonstrating no more than a 45% reduction in TOC production with respect to the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism experiences an increase in TOC. For example, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain can produce at least 25% or at least 50% more FAME lipids or at least 75% more FAME lipids with respect to a control microorganism while demonstrating no more than a 50% reduction in TOC production with respect to the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism experiences an increase in TOC. In various embodiments the mutant microorganism can display higher lipid productivity and/or carbon partitioning to lipid over a culture period of at least 3, at least 5, at least 7, at least 10, at least 12 days, at least 13, at least 15, at least 20, or at least 30 days. For example, mutant microorganism can have higher lipid productivity each day of the at least 5, at least 7, at least 10, at least 12 days, at least 15, at least 20, or at least 30-day culture period.

In some exemplary embodiments the amino acid sequence of the polypeptide having a Zn(2)Cys(6) domain is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identical to any of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. In some examples, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, or SEQ ID NO:17. For example, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or SEQ ID NO:17, or at least the N-terminal 517 amino acids of SEQ ID NO:2 or the N-terminal 540 amino acids of SEQ ID NO:17. In further examples a mutant microorganism as provided herein has attenuated expression of a gene encoding a polypeptide that includes an amino acid sequence having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NO:2, SEQ ID NO:17, SEQ ID NO:18, or SEQ ID NO:19, or to amino acids 1-200 of SEQ ID NO:20. In some examples, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or SEQ ID NO:17. Alternatively or in addition, a mutant microorganism as provided herein can have attenuated expression of a gene having a coding sequence with at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84. In various embodiments the microorganism is a diatom or eustigmatophyte alga, and in some examples may be a species of Nannochloropsis.

Alternatively or in addition to any of the above, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a polypeptide that has a Zn(2)Cys(6) domain and further includes a PAS3 domain. In some examples the PAS3 domain comprises an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25. The gene whose expression is attenuated can additionally encoding a polypeptide that further includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least 200 amino acids of any of SEQ ID NOs:18-20.

An attenuated gene encoding a polypeptide having a Zn(2)Cys(6) domain can be a gene that has an insertion, deletion, and/or one or more base changes with respect to the wild type gene. The insertion, deletion, or one or more base changes can be in a coding region, intron, 3′ untranslated region, or 5′ untranslated region of the gene, or can be upstream of the 5′ untranslated region of the gene, e.g., in the promoter region of a gene, where the mutant produces less of an RNA corresponding to the gene and/or produces less of the encoded polypeptide. Alternatively or in addition, a mutant microorganism as provided herein can include an antisense construct, an RNAi construct, a guide RNA (gRNA) as part of a CRISPR system, or a ribozyme that targets the gene encoding the polypeptide having a Zn(2)Cys(6) domain, resulting in reduced expression of the gene.

A mutant microorganism as provided herein can be any eukaryotic microorganism, and in some examples is a heterokont or alga. For example, the mutant microorganism can be a Labyrinthulomycte species, such as, for example, a species of Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia. Alternatively a mutant microorganism can be an algal species such as for example, a species belonging to any of the genera Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox. In some embodiments a mutant microorganism is a diatom or eustigmatophyte alga. In some embodiments the mutant microorganism is a species of Nannochloropsis.

A further aspect of the invention is a method of producing lipid, comprising culturing a mutant microorganism as provided herein and isolating lipid from the microorganism, the culture medium, or both. The mutant microorganism can be cultured in a medium that comprises less than about 5 mM ammonium, less than about 2.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM. The culture medium can include, for example, from about 0 to about 2.5 mM ammonium, from about 0.1 to about 2.5 mM ammonium, from about 0.5 to about 2.5 mM ammonium, from about 0 to about 1 mM ammonium, from about 0.1 to about 1 mM ammonium, or from about 0.2 to about 1 mM ammonium. The microorganism can be cultured in a medium that includes nitrate, which in some examples may be substantially the sole nitrogen source in the culture medium or may be present in addition to ammonium that may be present at a concentration of less than 5 mM, less than 2.5 mM, less than 2 mM, or less than 1 mM. Alternatively or in addition, the culture medium can comprise urea, which in some examples can be substantially the sole source of nitrogen in the culture medium. The mutant microorganism can be cultured under batch, continuous, or semi-continuous mode. The mutant microorganism can in some embodiments be a photosynthetic microorganism, e.g., and alga, and can be cultured photoautotrophically.

Yet another aspect of the invention is a method of producing lipid that includes culturing a microorganism under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, and isolating lipid from the microorganism, the culture medium, or both. For example, the microorganisms can be cultured such that the FAME to TOC ratio is maintained at between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. The ratio can be maintained at between about 0.3 and about 0.8, for example between about 0.4 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55 for at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15, at least 20, at least 30 days, or at least 60 days. The microorganism can be cultured under batch, continuous, or semi-continuous mode. The method of producing lipid can include culturing a mutant microorganism such as any provided herein under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. For example, the microorganism can be a mutant microorganism having attenuated expression of a Zn(2)Cys(6) regulator gene, such as but not limited to a gene encoding a polypeptide having at least 55%, at least 65%, at least 75%, or at least 85% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17. Alternatively or in addition, the microorganism can be a mutant microorganism having attenuated expression of a gene that has a coding sequence having at least 50%, at least 55%, at least 60%, least 65%, at least 70%, at least 75%, at least 80%, at least 85% at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:71-84. In any of the above methods for producing lipid, the mutant microorganism can be an alga, and the culturing can be under photoautotrophic conditions, i.e., conditions in which inorganic carbon is substantially the sole carbon source in the culture medium.

Yet another aspect of the invention is a nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide including an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. The polypeptide having at least 60% identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17 can include an amino acid sequence encoding a Zn(2)Cys(6) domain. The nucleic acid molecule in various examples can be or comprise a cDNA that lacks one or more introns present in the naturally-occurring gene, or, alternatively, can include one or more introns not present in the naturally-occurring gene. The nucleic acid molecule in various examples can have a sequence that is not 100% identical to a naturally-occurring gene. The nucleic acid molecule in various examples can comprise a heterologous promoter operably linked to the sequence encoding a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17 and/or can comprise a vector that includes a sequence encoding a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17.

A further aspect of the invention is a construct designed for attenuating expression of a gene encoding a polypeptide containing a Zn(2)Cys(6) domain. The construct can be or comprise, in various examples, a sequence encoding a guide RNA of a CRISPR system, an RNAi construct, an antisense construct, a ribozyme construct, or a construct for homologous recombination, e.g., a construct having one or more nucleotide sequences having homology to a naturally-occurring Zn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequences adjacent thereto in the native genome from which the gene is derived. For example, the construct can include at least a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequence homologous to at least a portion of an gene that encodes a polypeptide that includes an amino acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17. Alternatively or in addition, the construct can include a sequence having at least 50%, at least 55%, at least 60%, least 65%, at least 70%, at least 75%, at least 80%, at least 85% at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:71-84.

The construct can include, for example, at least a portion of the coding region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of an intron of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of a 5′UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, at least a portion of the promoter region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, and/or at least a portion of a 3′ UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain. In some examples, the construct can be an RNAi, ribozyme, or antisense construct and can include a sequence from the transcribed region of the gene encoding a polypeptide having a Zn(2)Cys(6) domain in either sense or antisense orientation. In further examples a construct can be designed for the in vitro or in vivo expression of a guide RNA (e.g., of a CRISPR system) designed to target a gene encoding a polypeptide having a Zn(2)Cys(6) domain, and can include a sequence homologous to a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, including, for example, an intron, a 5′UTR, a promoter region, and/or a 3′ UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain. In yet further examples, a construct for attenuating expression a gene encoding a Zn(2)Cys(6) domain-containing polypeptide can be a guide RNA of a CRISPR system or a CRISPRi system or can be an antisense oligonucleotide, where the sequence having homology to a transcribed region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain is in antisense orientation.

These and other objects and features of the invention will become more fully apparent when the following detailed description of the invention is read in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A provides a graph showing lipid (FAME) accumulation of wild-type Nannochloropsis cultures grown in N replete (+N) and deplete (−N) conditions. The 3-hour time point samples were subjected to transcriptomic analysis (RNA-seq). FIG. 1B provides a plot of the differentially expressed genes in cells transferred to −N medium compared to cells provided with N replete medium. The genes (represented as dots) are plotted versus fold change (log 2) in −N treated cells compared to replete cells. Putative transcription factors are represented as Xs. Genes present in the right side of the y-axis are upregulated and genes on the left side of the y-axis are downregulated. Only genes with a false discovery rate (FDR) less than or equal to 0.01 are displayed on the graph.

FIG. 2 is a schematic map of vector pSGE-6206 used to introduce the Cas9 gene into the N. gaditana Editor line.

FIG. 3A provides a map of the vector used in to generate the Cas9 expression strain Ng-CAS9+ in Nannochloropsis. FIG. 3B is an overlayed histogram from the Accuri C6 flow cytometer showing GFP fluorescence in the Ng-Cas9 editor strain (right peak, in red) compared to the wild type strain (left peak, in black). FIG. 3C is an image of a western blot with an anti-FLAG antibody demonstrating Cas9 expression in the Ng-CAS9+ line, with no background in the wild type control.

FIG. 4A provides a diagram of the donor fragment used for gene disruption at Cas9 target sites. The donor fragment construct includes the HygR (hygromycin resistance) gene driven by the EIF3 promoter and followed by the GNPDA terminator in inverted orientation. FIG. 4B is a schematic representation of a Cas9-mediated insertion of the hygromycin resistance (HygR) cassette into the ZnCys locus. The HygR cassette consisted of a promoter (Prom) driving the HygR gene followed by a terminator (T). The resulting mutant genotype (ZnCys-KO) was identified by PCR using primers that flank the insertion (arrows). The diagram is not to scale. FIG. 4C shows PCR genotyping of several Hyg resistant colonies transformed with a guide RNA designed to target the ZnCys locus. Presence of a 3 Kb band indicates insertion into the intended locus, while a 0.5 Kb band indicates an intact wild-type locus.

FIG. 5 is a schematic depiction of the N. gaditana ZnCys-2845 gene. A box denotes the position of the Zn(2)Cys(6) domain, which was the region targeted by the RNAi construct. Positions of insertions of the donor fragment in the BASH-3, knockout, and BASH-12 mutants are shown by arrows. The general location of the putative monopartite nuclear localization signal is also shown (NLS). The figure is not to scale.

FIG. 6A provides incident irradiance profiles for batch growth assessment and FIG. 6B is the Semi-continuous Productivity Assay.

FIG. 7A is a graph depicting FAME productivity of wild-type and ZnCys-2845 knockout N. gaditana cells cultured in batch mode in nitrate-only medium as determined from samples taken on odd days of the culture. FIG. 7B is a graph depicting TOC productivities for days 3-7 of the batch productivity assay. FIG. 7C is a graph depicting FAME/TOC ratios calculated from samples taken on odd days of the culture.

FIG. 7D is a bar graph depicting the amount of fatty acids of various chain lengths present in the lipid isolated on day 7 of the batch assay from wild type WT-3730 and ZnCys 2845 knockout strain GE-8564. FIG. 7E is a bar graph depicting the level of TAG isolated from wild type and ZnCys 2845 knockout strain GE-8564 on day 7 of the batch assay. FIG. 7F is an electron micrograph of a wild type Nannochloropsis gaditana cell cultured in nitrate-only (nitrogen-replete) culture medium. FIG. 7G is an electron micrograph of a Nannochloropsis gaditana ZnCys knockout mutant GE-8564 cell cultured in nitrate-only culture medium. FIG. 7H is an electron micrograph of a wild type Nannochloropsis gaditana cell cultured in nitrogen-deplete culture medium. Error bars in graphs represent the standard deviation for the average value of three cultures (biological replicates). Symbols used in graphs: asterisks represent wild type WT-3730 cultured in nitrate plus ammonium medium PM124, black diamonds represent knockout mutant GE-8564 cultured in nitrate plus ammonium medium PM124, X's represent wild type WT-3730 cultured in nitrate-only medium PM074, and black circles represent knockout mutant GE-8564 cultured in nitrate-only medium PM074. N: nucleus; Ch: chloroplast; LD: lipid droplet; M: mitochondrion.

FIGS. 8A-8B provide graphs demonstrating repression of the lipid accumulation phenotype of ZnCys-KO by NH₄ ⁺ supplementation in a five-day batch mode assay. FIG. 8A shows FAME (mg/L) per day. FIG. 8B shows TOC (mg/L) per day. FIG. 8C shows FAME/TOC values per day of ZnCys-KO (circles) and WT (diamonds) grown in batch mode on medium supplemented with NH₄ ⁺ (SM-NH₄ ⁺/NO₃ ⁻). Error bars are standard deviations of 2 biological replicates (n=2).

FIG. 9 is an alignment of the PAS3 domain sequences of N. gaditana ZnCys-2845 and the PAS3 domain sequences of the ZnCys-2845 orthologs of N. oceanica, N. oculata, N. sauna, and N. granulata.

FIG. 10 is an alignment of the N. gaditana polypeptide sequence encoded by the ZnCys-2845 gene and the N. oceanica polypeptide sequence encoded by the ortholog of the ZnCys-2845 gene, as well as partial N-terminal sequences of polypeptides encoded by orthologous genes in N. granulata, N. oculata, and N. salina.

FIGS. 11A-11C provide graphs depicting productivities of the N. gaditana wild type strain and GE-8564 knockout strain in a semi-continuous assay in which the culture medium includes urea as the sole nitrogen source. FIG. 11A shows daily FAME productivity over thirteen days of the assay. FIG. 11B shows daily TOC productivity over thirteen days of the assay. FIG. 11C) provides the FAME/TOC ratios for each day of the assay. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates). Symbols used in graphs: squares represent wild type WT-3730 cultured in urea-only medium PM125, triangles represent wild type WT-3730 cultured in nitrate-only medium PM074, circles represent ZnCys-2845 knockout mutant GE-8564 cultured in urea-only medium PM125, and diamonds represent ZnCys-2845 knockout mutant GE-8564 cultured in nitrate-only medium PM074.

FIG. 12A is a schematic depiction of the ZnCys-2845 gene with the positions of the nuclear localization signal (NLS), Zn(2)Cys(6) domain (Zn) and PAS3 domain shown as boxes and arrows depicting the sites of CRISPR-targeted mutations. FIG. 12B shows the relative transcript levels of the corresponding CRISPR-targeted mutants (position of primers used for transcript assessment shown in FIG. 12A. Normalized expression levels are relative to the average wild type level which was set to 1.0.

FIG. 13A is a graph depicting FAME productivity of wild-type and ZnCys-2845 knockdown N. gaditana cells cultured in batch mode in nitrate-only medium. FIG. 13B is a graph depicting TOC values for the odd days of the screen (days 1-3 and days 3-5). FIG. 13C is a graph providing FAME/TOC ratios of the cultures calculated on days 3, 5, and 7. Symbols used in graphs: open circles represent wild type WT-3730, a plus sign represents knockout mutant GE-13108, “BASH2”; an asterisk represents knockout mutant GE-13109, “BASH3”; Xs represent knockout mutant GE-13112, “BASH12”; open triangles represent ZnCys-2845 knockout mutant GE-8564; and dashes represent RNAi-7 strain GE-13103. The Error bars represent the standard deviation of two calculated productivity values of two separate cultures.

FIG. 14A provides the modular structure and salient features of the ZnCys locus. Abbreviations: NLS, nuclear localization sequence; Zn₂Cys₆, Zn(II)2Cys6 binuclear cluster domain (Pfam id: PF00172). The approximate location of the insertion in the original ZnCys-KO mutant is indicated with a black arrow. Patterned arrows indicate locations of successful Cas9 insertional mutants in putative 5′UTR (BASH-3 (strain GE-13109) ˜65 bp from the predicted start site) and 3′UTR regions (BASH-12 (strain GE-13112), approximately 30 bp from the predicted stop codon). Black horizontal arrows show the approximate location of the qRT-PCR primers used for assessing gene expression levels in panel B. The RNAi hairpin designed to silence ZnCys spanned the conserved Zn₂Cys₆ domain was homologous to the sequence denoted by the dotted double arrow. The figure is not to scale. FIG. 14B shows steady-state mRNA levels of the ZnCys locus in attenuated ZnCys lines (left to right on graph, wild type (WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO) relative to wild type (WT) as determined by qRT-PCR (left to right on graph, wild type (WT) ZnCys-BASH-3, ZnCys-BASH-12, ZnCys-RNAi-7, and ZnCys-KO). Expression levels were normalized to a housekeeping gene and were calculated relative to WT using the ΔΔC_(T) method. Error bars are standard errors for 3 technical replicates. FIG. 14C shows TOC productivity and FAME/TOC values of ZnCys mutant lines assessed in batch mode in nitrate-replete medium (SM-NO3-). Individual data points used to calculate FAME/TOC and biomass productivity averages are shown in FIGS. 15A-15B. Error bars are standard deviations of two biological replicates.

FIG. 15A is a batch mode assessment of FAME (mg/L) produced by ZnCys attenuated lines (ZnCys-BASH-3 (GE-13109), ZnCys-BASH-12 (GE-13112), ZnCys-RNAi-7 (GE-13103)) grown in nitrate-replete medium. FIG. 15B is a batch mode assessment of TOC (mg/L) measurements corresponding to days 3, 5 and 7 of the screen.

FIGS. 16A-16D provide graphs and a table depicting productivities of the N. gaditana wild type strain and GE-8564 knockout strain in a semi-continuous assay in which the culture medium used for daily dilution includes nitrate as the sole nitrogen source. FIG. 16A shows daily FAME productivity over thirteen days of the assay (mg/L culture). FIG. 16B provides the daily productivities of the cultures in g/m2/day (standard deviation of three cultures provided in parentheses), along with the average daily productivity for each culture. FIG. 16C shows daily TOC productivity over thirteen days of the assay (mg/L culture). FIG. 16D provides the FAME/TOC ratios for each day of the assay Symbols used in graphs: diamonds represent wild type WT-3730 pre-cultured in nitrate-only medium; Xs represent knockdown mutant GE-13108 “BASH2” pre-cultured in nitrate plus ammonium medium; triangles represent knockdown mutant GE-13109 “BASH3” pre-cultured in nitrate plus ammonium medium; squares represent knockdown mutant GE-13112 “BASH12” pre-cultured in nitrate plus ammonium medium; open circles represent knockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate plus ammonium medium; closed circles represent knockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate-only medium; and dashes represent knockout mutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

FIGS. 17A-17B. Productivity assessment of ZnCys mutants grown in semi-continuous mode for 8 days on NO₃ ⁻-containing culture medium. FIG. 17A shows daily FAME and FIG. 17B shows TOC (mg/L) measurements for ZnCys mutants (ZnCys-RNAi-7, ZnCys-BASH-12 and ZnCys-BASH-3) compared to their parental lines Ng-CAS9+ and WT. Cultures were grown in semi-continuous mode at a 30% daily dilution rate on SM-NO₃ ⁻. Error bars represent standard deviations for 3 biological replicates (n=3).

FIG. 18 provides a bar graph of FAME and TOC productivities (g/m²/day) of ZnCys mutants (ZnCys-RNAi-7 (GE-13103), ZnCys-BASH-12 (GE-13112) and ZnCys-BASH-3 (GE-13109)) compared to their parental lines Ng-CAS9+(GE-6791) and WT in the assay whose daily FAME and TOC productivities are depicted in FIGS. 17A-17B. Productivity values are 8-day averages of daily measurements (n=3).

FIG. 19 provides a graph depicting the daily nitrogen content of the cells (mg/L culture, pellets only) in the semi-continuous assay whose daily FAME and TOC productivities are provided in FIGS. 16A-16D. Symbols used in graphs: diamonds represent wild type WT-3730 pre-cultured in nitrate-only medium; Xs represent knockdown mutant GE-13108 “BASH2” pre-cultured in nitrate plus ammonium medium; triangles represent knockdown mutant GE-13109 “BASH3” pre-cultured in nitrate plus ammonium medium; squares represent knockdown mutant GE-13112 “BASH12” pre-cultured in nitrate plus ammonium medium; open circles represent knockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate plus ammonium medium; closed circles represent knockdown mutant GE-13103 “RNAi-7” pre-cultured in nitrate-only medium; and dashes represent knockout mutant GE-8564 pre-cultured in nitrate plus ammonium medium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

FIG. 20 provides a graph depicting total nitrogen and FAME levels of cultures of N. gaditana wild type strain WT-3730 and RNAi mutant GE-13103 in a semi-continuous assay using nitrate-only media, in which the GE-13103 knockdown strain was pre-cultured separately in either PM124 medium that included both nitrate and ammonium or in PM074 medium that included only nitrate. Wild type strain WT-3730 was pre-cultured in PM074 medium that included only nitrate. Solid diamonds and solid triangles represent the total nitrogen content of the cultures (cells plus culture medium) of GE-13103 pre-cultured in PM124 and PM074, respectively. Open diamonds and open triangles represent the FAME content of the cultures of GE-13103 pre-cultured in PM124 and PM074, respectively. Solid squares represent the FAME content of a culture of WT-3730 pre-cultured in nitrate-only medium. The calculated amount of ammonium on three days of the productivity assay is noted on the graph.

FIGS. 21A-21F provides graphs and a table depicting productivities of the N. gaditana wild type strain WT-3730 and GE-13103 knockdown strain in a semi-continuous assay in which the culture medium included three different concentrations of ammonium. FIG. 21A depicts FAME productivity (mg/L) in the semi-continuous assay in culture in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21B provides daily FAME productivities (g/m²/day) (standard deviation of three cultures provided in parentheses), along with the average daily productivity for each culture condition in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21C depicts TOC productivity (mg/L) in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21D provides daily TOC productivities (g/m²/day) (standard deviation of three cultures for each ammonium concentration provided in parentheses), along with the average daily productivity for each culture condition in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21E depicts daily FAME/TOC ratios in the semi-continuous assay in which the ammonium level of the media used throughout the assay was 2.5, 1.0, or 0.5 mM. FIG. 21F provides daily cell counts determined by flow cytometry of cultures analyzed for FAME and TOC productivities in FIGS. 21A-21E. Symbols used in graphs: Circles: WT-3730 cultured in nitrate-only medium; Squares: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 2.5 mM ammonium; Triangles: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 1.0 mM ammonium; Xs: RNAi knockdown strain GE-13103 cultured in nitrate-containing medium that also included 0.5 mM ammonium. Error bars in graphs represent the standard deviation of the three independent cultures (biological replicates).

FIGS. 22A-22E. Productivity assessment of ZnCys-KO and ZnCys-RNAi-7 grown in semi-continuous mode on nitrate-containing medium. FIG. 22A depicts daily FAME (mg/L). FIG. 22B depicts daily TOC (mg/L). FIG. 22C depicts C/N values derived from cellular N-content. FIG. 22D provides a bar graph comparing FAME. FIG. 22E depicts TOC productivities (g/m²/day) for WT and ZnCys-RNAi-7 calculated for the entire 13-day assay. ZnCys-KO failed to reach steady-state at a 30% daily dilution scheme and essentially washed away as the run progressed, therefore lipid and biomass productivity values were not calculated for this line (N/A, not available). ZnCys-KO was scaled up in culture medium that included NH₄ ⁺ in addition to NO₃ ⁻ to obtain enough biomass for the assay.

FIG. 23 is a bar graph depicting the biomolecular composition of wild type Nannochloropsis strain WT-3730 and two ZnCys knockdown mutants, GE-13112 (BASH 12) and GE-13130 (RNAi).

FIG. 24 depicts hierarchical clustering by Euclidian distance of transcriptional fold changes of genes encoding proteins involved in N-assimilation from biological triplicates of ZnCys-KO, the nitrate reductase knockout mutant (NR-KO), RNAi-7 and WT grown in batch mode on nitrate-only medium (NO₃, light green) or medium that included both ammonium and nitrate (NH₄, dark green). Red indicates increased expression and blue indicates reduced expression, with black being neutral (neither increased nor decreased).

FIG. 25 provides images of immunoblot analysis of enzymes in the FAS cycle (KAR1, KAS1/3, HAD and ENR), acetyl-CoA carboxylase (ACCase), glutamate synthase (GOGAT2) and nitrate reductase (NR) for duplicate cultures grown in batch mode on nitrate-only medium (WT, ZnCys-KO and ZnCys-RNAi-7 shown as RNAi-7). Coomassie brilliant blue stain (CBB) of a protein gel used for blotting is shown as a loading reference.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application including the definitions will control. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All ranges provided within the application are inclusive of the values of the upper and lower ends of the range unless specifically indicated otherwise.

All publications, patents and other references mentioned herein are incorporated by reference in their entireties for all purposes as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

The term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B”, “A or B”, “A”, and “B”.

“About” means either within 10% of the stated value, or within 5% of the stated value, or in some cases within 2.5% of the stated value, or, “about” can mean rounded to the nearest significant digit.

The term “gene” is used broadly to refer to any segment of a nucleic acid molecule (typically DNA, but optionally RNA) encoding a polypeptide or expressed RNA. Thus, genes include sequences encoding expressed RNA (which can include polypeptide coding sequences or, for example, functional RNAs, such as ribosomal RNAs, tRNAs, antisense RNAs, microRNAs, short hairpin RNAs, ribozymes, etc.). Genes may further comprise regulatory sequences required for or affecting their expression, as well as sequences associated with the protein or RNA-encoding sequence in its natural state, such as, for example, intron sequences, 5′ or 3′ untranslated sequences, etc. In some examples, “gene” may only refer to a protein-encoding portion of a DNA or RNA molecule, which may or may not include introns. A gene is preferably greater than 50 nucleotides in length, more preferably greater than 100 nucleotides in length, and can be, for example, between 50 nucleotides and 500,000 nucleotides in length, such as between 100 nucleotides and 100,000 nucleotides in length or between about 200 nucleotides and about 50,000 nucleotides in length, or about 200 nucleotides and about 20,000 nucleotides in length. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information.

The term “nucleic acid” or “nucleic acid molecule” refers to, a segment of DNA or RNA (e.g., mRNA), and also includes nucleic acids having modified backbones (e.g., peptide nucleic acids, locked nucleic acids) or modified or non-naturally-occurring nucleobases. The nucleic acid molecules can be double-stranded or single-stranded; a single stranded nucleic acid molecule that comprises a gene or a portion thereof can be a coding (sense) strand or a non-coding (antisense) strand.

A nucleic acid molecule may be “derived from” an indicated source, which includes the isolation (in whole or in part) of a nucleic acid segment from an indicated source. A nucleic acid molecule may also be derived from an indicated source by, for example, direct cloning, PCR amplification, or artificial synthesis from the indicated polynucleotide source or based on a sequence associated with the indicated polynucleotide source, which may be, for example, a species of organism. Genes or nucleic acid molecules derived from a particular source or species also include genes or nucleic acid molecules having sequence modifications with respect to the source nucleic acid molecules. For example, a gene or nucleic acid molecule derived from a source (e.g., a particular referenced gene) can include one or more mutations with respect to the source gene or nucleic acid molecule that are unintended or that are deliberately introduced, and if one or more mutations, including substitutions, deletions, or insertions, are deliberately introduced the sequence alterations can be introduced by random or targeted mutation of cells or nucleic acids, by amplification or other gene synthesis or molecular biology techniques, or by chemical synthesis, or any combination thereof. A gene or nucleic acid molecule that is derived from a referenced gene or nucleic acid molecule that encodes a functional RNA or polypeptide can encode a functional RNA or polypeptide having at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%, sequence identity with the referenced or source functional RNA or polypeptide, or to a functional fragment thereof. For example, a gene or nucleic acid molecule that is derived from a referenced gene or nucleic acid molecule that encodes a functional RNA or polypeptide can encode a functional RNA or polypeptide having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the referenced or source functional RNA or polypeptide, or to a functional fragment thereof.

As used herein, an “isolated” nucleic acid or protein is removed from its natural milieu or the context in which the nucleic acid or protein exists in nature. For example, an isolated protein or nucleic acid molecule is removed from the cell or organism with which it is associated in its native or natural environment. An isolated nucleic acid or protein can be, in some instances, partially or substantially purified, but no particular level of purification is required for isolation. Thus, for example, an isolated nucleic acid molecule can be a nucleic acid sequence that has been excised from the chromosome, genome, or episome that it is integrated into in nature, or has been synthesized apart from other sequences of the chromosome, genome, or episome that it is associated with in nature, or has been synthesized apart from other sequences with which it is juxtaposed in nature.

A “purified” nucleic acid molecule or nucleotide sequence, or protein or polypeptide sequence, is substantially free of cellular material and cellular components. The purified nucleic acid molecule or protein may be substantially free of chemicals beyond buffer or solvent, for example. “Substantially free” is not intended to mean that other components beyond the novel nucleic acid molecules are undetectable.

The terms “naturally-occurring” and “wild type” refer to a form found in nature. For example, a naturally occurring or wild type nucleic acid molecule, nucleotide sequence or protein may be present in and isolated from a natural source, and is not intentionally modified by human manipulation.

As used herein “attenuated” means reduced in amount, degree, intensity, or strength with respect to a control that does not have the manipulation or mutation that results in attenuated expression or activity. Attenuated gene expression may refer to a significantly reduced amount and/or rate of transcription of the gene in question, or of translation, folding, or assembly of the encoded protein. As nonlimiting examples, an attenuated gene may be an endogenous gene of the organism that is mutated or disrupted (e.g., a gene disrupted by partial or total deletion, truncation, frameshifting, or insertional mutation) that does not encode a complete functional open reading frame or that has decreased expression due to alteration or disruption of gene regulatory sequences. An attenuated gene may also be a gene targeted by a construct that reduces expression of the gene, such as, for example, an antisense RNA, microRNA, RNAi molecule, or ribozyme. Attenuated gene expression can be gene expression that is eliminated, for example, reduced to an amount that is insignificant or undetectable, or can be gene expression the is reduced by any amount with respect to the gene expression of a control microorganism, for example reduced from about 1% to about 99%, or from about 5% to about 95% of the level of gene expression of the control microorganism. Attenuated gene expression can also be gene expression that results in an RNA or protein that is not fully functional or nonfunctional, for example, attenuated gene expression can be gene expression that results in a truncated RNA and/or polypeptide.

“Exogenous nucleic acid molecule” or “exogenous gene” refers to a nucleic acid molecule or gene that has been introduced (“transformed”) into a cell. A transformed cell may be referred to as a recombinant cell, into which additional exogenous gene(s) may be introduced. A descendent of a cell transformed with a nucleic acid molecule is also referred to as “transformed” if it has inherited the exogenous nucleic acid molecule. The exogenous gene may be from a different species (and so “heterologous”), or from the same species (and so “homologous”), relative to the cell being transformed. An “endogenous” nucleic acid molecule, gene or protein is a native nucleic acid molecule, gene or protein as it occurs in, or is naturally produced by, the host.

The term “native” is used herein to refer to nucleic acid sequences or amino acid sequences as they naturally occur in the host. The term “non-native” is used herein to refer to nucleic acid sequences or amino acid sequences that do not occur naturally in the host. A nucleic acid sequence or amino acid sequence that has been removed from a cell, subjected to laboratory manipulation, and introduced or reintroduced into a host cell such that it differs in sequence or location in the genome with respect to its position in a non-manipulated organism (i.e., is juxtaposed with or operably linked to sequences it is not juxtaposed with or operably linked to in a non-transformed organism) is considered “non-native”. Thus non-native genes include genes endogenous to the host microorganism operably linked to one or more heterologous regulatory sequences that have been recombined into the host genome.

A “recombinant” or “engineered” nucleic acid molecule is a nucleic acid molecule that has been altered through human manipulation. As non-limiting examples, a recombinant nucleic acid molecule includes any nucleic acid molecule that: 1) has been partially or fully synthesized or modified in vitro, for example, using chemical or enzymatic techniques (e.g., by use of chemical nucleic acid synthesis, or by use of enzymes for the replication, polymerization, digestion (exonucleolytic or endonucleolytic), ligation, reverse transcription, transcription, base modification (including, e.g., methylation), integration or recombination (including homologous and site-specific recombination) of nucleic acid molecules); 2) includes conjoined nucleotide sequences that are not conjoined in nature; 3) has been engineered using molecular cloning techniques such that it lacks one or more nucleotides with respect to the naturally occurring nucleic acid molecule sequence; and/or 4) has been manipulated using molecular cloning techniques such that it has one or more sequence changes or rearrangements with respect to the naturally occurring nucleic acid sequence. As non-limiting examples, a cDNA is a recombinant DNA molecule, as is any nucleic acid molecule that has been generated by in vitro polymerase reaction(s), or to which linkers have been attached, or that has been integrated into a vector, such as a cloning vector or expression vector.

The term “recombinant protein” as used herein refers to a protein produced by genetic engineering regardless of whether the amino acid sequence varies from that of a wild-type protein.

When applied to organisms, the term recombinant, engineered, or genetically engineered refers to organisms that have been manipulated by introduction of a heterologous or exogenous recombinant nucleic acid sequence into the organism, and includes gene knockouts, targeted mutations, gene replacement, and promoter replacement, deletion, or insertion, as well as introduction of transgenes or synthetic genes into the organism. Recombinant or genetically engineered organisms can also be organisms into which constructs for gene “knockdown” have been introduced. Such constructs include, but are not limited to, RNAi, microRNA, shRNA, siRNA, antisense, and ribozyme constructs. Also included are organisms whose genomes have been altered by the activity of meganucleases, zinc finger nucleases, TALENs, or cas/CRISPR systems. An exogenous or recombinant nucleic acid molecule can be integrated into the recombinant/genetically engineered organism's genome or in other instances may not be integrated into the host genome. As used herein, “recombinant microorganism” or “recombinant host cell” includes progeny or derivatives of the recombinant microorganisms of the invention. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny or derivatives may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

The term “promoter” refers to a nucleic acid sequence capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3′ direction) coding sequence. A promoter includes the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. A promoter can include a transcription initiation site as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. Eukaryotic promoters often, but not always, contain “TATA” boxes and “CAT” boxes. Prokaryotic promoters may contain −10 and −35 prokaryotic promoter consensus sequences. A large number of promoters, including constitutive, inducible and repressible promoters, from a variety of different sources are well known in the art. Representative sources include for example, algal, viral, mammalian, insect, plant, yeast, and bacterial cell types, and suitable promoters from these sources are readily available, or can be made synthetically, based on sequences publicly available on line or, for example, from depositories such as the ATCC as well as other commercial or individual sources. Promoters can be unidirectional (initiate transcription in one direction) or bi-directional (initiate transcription in either direction). A promoter may be a constitutive promoter, a repressible promoter, or an inducible promoter. A promoter region can include, in addition to the gene-proximal promoter where RNA polymerase binds to initiate transcription, additional sequences upstream of the gene that can be within 1 kb, 2 kb, 3 kb, 4 kb, 5 kb or more of the transcriptional start site of a gene, where the additional sequences can influence the rate of transcription of the downstream gene and optionally the responsiveness of the promoter to developmental, environmental, or biochemical (e.g., metabolic) conditions.

The term “heterologous” when used in reference to a polynucleotide, gene, nucleic acid, polypeptide, or enzyme refers to a polynucleotide, gene, nucleic acid, polypeptide, or enzyme that is from a source or derived from a source other than the host organism species. In contrast a “homologous” polynucleotide, gene, nucleic acid, polypeptide, or enzyme is used herein to denote a polynucleotide, gene, nucleic acid, polypeptide, or enzyme that is derived from the host organism species. When referring to a gene regulatory sequence or to an auxiliary nucleic acid sequence used for maintaining or manipulating a gene sequence (e.g., a promoter, a 5′ untranslated region, 3′ untranslated region, poly A addition sequence, intron sequence, splice site, ribosome binding site, internal ribosome entry sequence, genome homology region, recombination site, etc.), “heterologous” means that the regulatory sequence or auxiliary sequence is not naturally associated with the gene with which the regulatory or auxiliary nucleic acid sequence is juxtaposed in a construct, genome, chromosome, or episome. Thus, a promoter operably linked to a gene to which it is not operably linked to in its natural state (i.e., in the genome of a non-genetically engineered organism) is referred to herein as a “heterologous promoter,” even though the promoter may be derived from the same species (or, in some cases, the same organism) as the gene to which it is linked.

As used herein, the term “protein” or “polypeptide” is intended to encompass a singular “polypeptide” as well as plural “polypeptides,” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds). The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, peptides, dipeptides, tripeptides, oligopeptides, “protein,” “amino acid chain,” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide,” and the term “polypeptide” can be used instead of, or interchangeably with any of these terms.

Gene and protein Accession numbers, commonly provided in parenthesis after a gene or species name, are unique identifiers for a sequence record publicly available at the National Center for Biotechnology Information (NCBI) website (ncbi.nlm.nih.gov) maintained by the United States National Institutes of Health. The “GenInfo Identifier” (GI) sequence identification number is specific to a nucleotide or amino acid sequence. If a sequence changes in any way, a new GI number is assigned. A Sequence Revision History tool is available to track the various GI numbers, version numbers, and update dates for sequences that appear in a specific GenBank record. Searching and obtaining nucleic acid or gene sequences or protein sequences based on Accession numbers and GI numbers is well known in the arts of, e.g., cell biology, biochemistry, molecular biology, and molecular genetics.

As used herein, the terms “percent identity” or “homology” with respect to nucleic acid or polypeptide sequences are defined as the percentage of nucleotide or amino acid residues in the candidate sequence that are identical with the known polypeptides, after aligning the sequences for maximum percent identity and introducing gaps, if necessary, to achieve the maximum percent homology. N-terminal or C-terminal insertion or deletions shall not be construed as affecting homology, and internal deletions and/or insertions into the polypeptide sequence of less than about 50, less than about 40, less than about 30, less than about 20, or less than about 10 amino acid residues shall not be construed as affecting homology. Homology or identity at the nucleotide or amino acid sequence level can be determined by BLAST (Basic Local Alignment Search Tool) analysis using the algorithm employed by the programs blastp, blastn, blastx, tblastn, and tblastx (Altschul (1997), Nucleic Acids Res. 25, 3389-3402, and Karlin (1990), Proc. Natl. Acad. Sci. USA 87, 2264-2268), which are tailored for sequence similarity searching. The approach used by the BLAST program is to first consider similar segments, with and without gaps, between a query sequence and a database sequence, then to evaluate the statistical significance of all matches that are identified, and finally to summarize only those matches which satisfy a preselected threshold of significance. For a discussion of basic issues in similarity searching of sequence databases, see Altschul (1994), Nature Genetics 6, 119-129. The search parameters for histogram, descriptions, alignments, expect (i.e., the statistical significance threshold for reporting matches against database sequences), cutoff, matrix, and filter (low complexity) can be at the default settings. The default scoring matrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62 matrix (Henikoff (1992), Proc. Natl. Acad. Sci. USA 89, 10915-10919), recommended for query sequences over 85 in length (nucleotide bases or amino acids).

For blastn, designed for comparing nucleotide sequences, the scoring matrix can be set by the ratios of M (i.e., the reward score for a pair of matching residues) to N (i.e., the penalty score for mismatching residues), wherein the default values for M and N can be +5 and −4, respectively. Four blastn parameters can be adjusted as follows: Q=10 (gap creation penalty); R=10 (gap extension penalty); wink=1 (generates word hits at every winkth position along the query); and gapw=16 (sets the window width within which gapped alignments are generated). The equivalent Blastp parameter settings for comparison of amino acid sequences can be: Q=9; R=2; wink=1; and gapw=32. A Bestfit comparison between sequences, available in the GCG package version 10.0, can use DNA parameters GAP=50 (gap creation penalty) and LEN=3 (gap extension penalty), and the equivalent settings in protein comparisons can be GAP=8 and LEN=2. The preceding parameter settings are exemplary only and other parameter settings may be used.

Thus, when referring to the polypeptide or nucleic acid sequences of the present invention, included are sequence identities of at least 40%, at least 45%, at least 50%, at least 55%, of at least 70%, at least 65%, at least 70%, at least 75%, at least 80%, or at least 85%, for example at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or about 100% sequence identity with the full-length polypeptide or nucleic acid sequence, or to fragments thereof comprising a consecutive sequence of at least 50, at least 75, at least 100, at least 125, at least 150, at least 200, or more than 200 amino acid residues of the entire protein; variants of such sequences, e.g., wherein at least one amino acid residue has been inserted N- and/or C-terminal to, and/or within, the disclosed sequence(s) which contain(s) the insertion and substitution. Contemplated variants can additionally or alternately include those containing predetermined mutations by, e.g., homologous recombination or site-directed or PCR mutagenesis, and the corresponding polypeptides or nucleic acids of other species, including, but not limited to, those described herein, the alleles or other naturally occurring variants of the family of polypeptides or nucleic acids which contain an insertion and substitution; and/or derivatives wherein the polypeptide has been covalently modified by substitution, chemical, enzymatic, or other appropriate means with a moiety other than a naturally occurring amino acid which contains the insertion and substitution (for example, a detectable moiety such as an enzyme).

As used herein, the phrase “conservative amino acid substitution” or “conservative mutation” refers to the replacement of one amino acid by another amino acid with a common property. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz (1979) Principles of Protein Structure, Springer-Verlag). According to such analyses, groups of amino acids can be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz (1979) Principles of Protein Structure, Springer-Verlag). Examples of amino acid groups defined in this manner can include: a “charged/polar group” including Glu, Asp, Asn, Gln, Lys, Arg, and His; an “aromatic or cyclic group” including Pro, Phe, Tyr, and Trp; and an “aliphatic group” including Gly, Ala, Val, Leu, Ile, Met, Ser, Thr, and Cys. Within each group, subgroups can also be identified. For example, the group of charged/polar amino acids can be sub-divided into sub-groups including: the “positively-charged sub-group” comprising Lys, Arg and His; the “negatively-charged sub-group” comprising Glu and Asp; and the “polar sub-group” comprising Asn and Gln. In another example, the aromatic or cyclic group can be sub-divided into sub-groups including: the “nitrogen ring sub-group” comprising Pro, His, and Trp; and the “phenyl sub-group” comprising Phe and Tyr. In another further example, the aliphatic group can be sub-divided into sub-groups including: the “large aliphatic non-polar sub-group” comprising Val, Leu, and Ile; the “aliphatic slightly-polar sub-group” comprising Met, Ser, Thr, and Cys; and the “small-residue sub-group” comprising Gly and Ala. Examples of conservative mutations include amino acid substitutions of amino acids within the sub-groups above, such as, but not limited to: Lys for Arg or vice versa, such that a positive charge can be maintained; Glu for Asp or vice versa, such that a negative charge can be maintained; Ser for Thr or vice versa, such that a free —OH can be maintained; and Gln for Asn or vice versa, such that a free —NH2 can be maintained. A “conservative variant” is a polypeptide that includes one or more amino acids that have been substituted to replace one or more amino acids of the reference polypeptide (for example, a polypeptide whose sequence is disclosed in a publication or sequence database, or whose sequence has been determined by nucleic acid sequencing) with an amino acid having common properties, e.g., belonging to the same amino acid group or sub-group as delineated above.

As used herein, “expression” includes the expression of a gene at least at the level of RNA production, and an “expression product” includes the resultant product, e.g., a polypeptide or functional RNA (e.g., a ribosomal RNA, a tRNA, a guide RNA, an antisense RNA, a micro RNA, an shRNA, a ribozyme, etc.), of an expressed gene. The term “increased expression” includes an alteration in gene expression to facilitate increased mRNA production and/or increased polypeptide expression. “Increased production” [of a gene product] includes an increase in the amount of polypeptide expression, in the level of the enzymatic activity of a polypeptide, or a combination of both, as compared to the native production or enzymatic activity of the polypeptide.

Some aspects of the present invention include the partial, substantial, or complete deletion, silencing, inactivation, or down-regulation of expression of particular polynucleotide sequences. The genes may be partially, substantially, or completely deleted, silenced, inactivated, or their expression may be down-regulated in order to affect the activity performed by the polypeptide they encode, such as the activity of an enzyme. Genes can be partially, substantially, or completely deleted, silenced, inactivated, or down-regulated by insertion of nucleic acid sequences that disrupt the function and/or expression of the gene (e.g., viral insertion, transposon mutagenesis, meganuclease engineering, homologous recombination, or other methods known in the art). The terms “eliminate,” “elimination,” and “knockout” can be used interchangeably with the terms “deletion,” “partial deletion,” “substantial deletion,” or “complete deletion” and refer to substantially eliminating expression of the gene, for example, reducing the level of expression to less than 10%, less than 5%, less than 2%, or less than 1% of control levels or undetectable levels. The terms “attenuation” and “knockdown” can be used to describe mutations and manipulations resulting in a lower level of expression of a gene with respect to wild type levels of expression, or, in some cases, resulting in reduced activity of a gene product, such as by mutating a functional domain of the encoded polypeptide. Attenuation can be complete attenuation (e.g., “knockout”) or can be partial attenuation, where, for example, RNA or protein levels are reduced or “knocked down” by from 1-99.5% of control levels, e.g., to a level where RNA or protein expression is detectable but reduced with respect to controls. In certain embodiments, a microorganism of interest may be engineered by site directed homologous recombination to knockout a particular gene of interest. In still other embodiments, RNAi or antisense DNA (asDNA) constructs may be used to partially, substantially, or completely silence, inactivate, or down-regulate a particular gene of interest.

These insertions, deletions, or other modifications of certain nucleic acid molecules or particular polynucleotide sequences may be understood to encompass “genetic modification(s)” or “transformation(s)” such that the resulting strains of the microorganisms or host cells may be understood to be “genetically modified”, “genetically engineered” or “transformed.”

As used herein, “up-regulated” or “up-regulation” includes an increase in expression of a gene or nucleic acid molecule of interest or the activity of an enzyme, e.g., an increase in gene expression or enzymatic activity as compared to the expression or activity in an otherwise identical gene or enzyme that has not been up-regulated.

As used herein, “down-regulated” or “down-regulation” includes a decrease in expression of a gene or nucleic acid molecule of interest or the activity of an enzyme, e.g., a decrease in gene expression or enzymatic activity as compared to the expression or activity in an otherwise identical gene or enzyme that has not been down-regulated.

As used herein, “mutant” refers to an organism that has a mutation in a gene that is the result of classical mutagenesis, for example, using gamma irradiation, UV, or chemical mutagens. “Mutant” as used herein also refers to a recombinant cell that has altered structure or expression of a gene as a result of genetic engineering that many include, as non-limiting examples, overexpression, including expression of a gene under different temporal, biological, or environmental regulation and/or to a different degree than occurs naturally and/or expression of a gene that is not naturally expressed in the recombinant cell; homologous recombination, including knock-outs and knock-ins (for example, gene replacement with genes encoding polypeptides having greater or lesser activity than the wild type polypeptide, and/or dominant negative polypeptides); gene attenuation via RNAi, antisense RNA, or ribozymes, or the like; and genome engineering using meganucleases, TALENs, and/or CRISPR technologies, and the like. A mutant is therefore not a naturally-occurring organism. A mutant organism of interest will typically have a phenotype different than that of the corresponding wild type or progenitor strain that lacks the mutation, where the phenotype can be assessed by growth assays, product analysis, photosynthetic properties, biochemical assays, etc. When referring to a gene “mutant” means the gene has at least one base (nucleotide) change, deletion, or insertion with respect to a native or wild type gene. The mutation (change, deletion, and/or insertion of one or more nucleotides) can be in the coding region of the gene or can be in an intron, 3′ UTR, 5′ UTR, or promoter region, e.g., within 2 kb of the transcriptional start site or within 3 kb or the translational start site. As nonlimiting examples, a mutant gene can be a gene that has an insertion within the promoter region that can either increase or decrease expression of the gene; can be a gene that has a deletion, resulting in production of a nonfunctional protein, truncated protein, dominant negative protein, or no protein; can be a gene that has one or more point mutations leading to a change in the amino acid of the encoded protein or results in aberrant splicing of the gene transcript, etc.

The term “Pfam” refers to a large collection of protein domains and protein families maintained by the Pfam Consortium and available at several sponsored world wide web sites, including: pfam.xfam.org/(European Bioinformatics Institute (EMBL-EBI). The latest release of Pfam is Pfam 30.0 (June 2016). Pfam domains and families are identified using multiple sequence alignments and hidden Markov models (HMMs). Pfam-A family or domain assignments, are high quality assignments generated by a curated seed alignment using representative members of a protein family and profile hidden Markov models based on the seed alignment. (Unless otherwise specified, matches of a queried protein to a Pfam domain or family are Pfam-A matches.) All identified sequences belonging to the family are then used to automatically generate a full alignment for the family (Sonnhammer (1998) Nucleic Acids Research 26, 320-322; Bateman (2000) Nucleic Acids Research 26, 263-266; Bateman (2004) Nucleic Acids Research 32, Database Issue, D138-D141; Finn (2006) Nucleic Acids Research Database Issue 34, D247-251; Finn (2010) Nucleic Acids Research Database Issue 38, D211-222). By accessing the Pfam database, for example, using the above-referenced website, protein sequences can be queried against the HMMs using HMMER homology search software (e.g., HMMER2, HMMER3, or a higher version, hmmer.org). Significant matches that identify a queried protein as being in a pfam family (or as having a particular Pfam domain) are those in which the bit score is greater than or equal to the gathering threshold for the Pfam domain. Expectation values (e values) can also be used as a criterion for inclusion of a queried protein in a Pfam or for determining whether a queried protein has a particular Pfam domain, where low e values (much less than 1.0, for example less than 0.1, or less than or equal to 0.01) represent low probabilities that a match is due to chance.

A “cDNA” is a DNA molecule that comprises at least a portion the nucleotide sequence of an mRNA molecule, with the exception that the DNA molecule substitutes the nucleobase thymine, or T, in place of uridine, or U, occurring in the mRNA sequence. A cDNA can be double stranded or single stranded and can be, for example, the complement of the mRNA sequence. In preferred examples, a cDNA does not include one or more intron sequences that occur in the naturally-occurring gene that the cDNA corresponds to (i.e., the gene as it occurs in the genome of an organism). For example, a cDNA can have sequences from upstream of an intron of a naturally-occurring gene juxtaposed to sequences downstream of the intron of the naturally-occurring gene, where the upstream and downstream sequences are not juxtaposed in a DNA molecule in nature (i.e., the sequences are not juxtaposed in the naturally occurring gene). A cDNA can be produced by reverse transcription of mRNA molecules, or can be synthesized, for example, by chemical synthesis and/or by using one or more restriction enzymes, one or more ligases, one or more polymerases (including, but not limited to, high temperature tolerant polymerases that can be used in polymerase chain reactions (PCRs)), one or more recombinases, etc., based on knowledge of the cDNA sequence, where the knowledge of the cDNA sequence can optionally be based on the identification of coding regions from genome sequences or compiled from the sequences multiple partial cDNAs.

Reference to properties that are “substantially the same” or “substantially identical” without further explanation of the intended meaning, is intended to mean the properties are within 10%, and preferably within 5%, and may be within 2.5%, within 1%, or within 0.5% of the reference value. Where the intended meaning of “substantially” in a particular context is not set forth, the term is used to include minor and irrelevant deviations that are not material to the characteristics considered important in the context of the invention.

Although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and are not intended to be limiting. Other features and advantages of the invention will be apparent from the detailed description and from the claims.

A “control cell” or “control microorganism” is a cell or microorganism that is substantially identical to the manipulated, recombinant, or mutant cell referred to, with the exception that the control cell does not have the modification of the manipulated, recombinant, or mutant cell. A control cell can be a wild type cell, for example a wild type cell of the strain from which the manipulated, recombinant, or mutant cell is directly or indirectly derived.

“The same conditions” or “the same culture conditions”, as used herein, means substantially the same conditions, that is, any differences between the referenced conditions are minor and not relevant to the function or properties of the microorganism that are material to the invention, e.g., lipid production or biomass production.

“Nitrogen replete” conditions, with respect to a particular cell type, are conditions under which the cell does not experience growth deficiency due to insufficient nitrogen.

As used herein “lipid” or “lipids” refers to fats, waxes, fatty acids, fatty acid derivatives such as fatty alcohols, wax esters, alkanes, and alkenes, sterols, monoglycerides, diglycerides, triglycerides, phospholipids, sphingolipids, saccharolipids, and glycerolipids. “FAME lipids” or “FAME” refers to lipids having acyl moieties that can be derivatized to fatty acid methyl esters, such as, for example, monoacylglycerides, diacylglycerides, triacylglycerides, wax esters, and membrane lipids such as phospholipids, galactolipids, etc. Lipid productivity can be assessed as FAME productivity in milligrams per liter (mg/L) over a given time period (e.g., per day) and for algae, may be reported as areal productivity, for example grams per meter² per day (g/m²/day). In the semi-continuous assays provided herein, mg/L/day values are converted to g/m2/day by taking into account the area of incident irradiance (the SCPA flask rack aperture of 1½″×33/8″, or 0.003145 m²) and the volume of the culture (550 ml). To obtain productivity values in g/m2/day, mg/L/day values are multiplied by the daily dilution rate (30%) and a conversion factor of 0.175. Where lipid or subcategories thereof (for example, TAG or FAME) are referred to as a percentage, the percentage is a weight percent unless indicated otherwise.

“Biomass” refers to cellular mass, whether of living or dead cells, and can be assessed, for example, as aspirated pellet weight, but is more preferably dry weight (e.g., lyophilate of a culture sample or pelleted cells), ash-free dry weight (AFDW), or total organic carbon (TOC), using methods known in the art. Biomass increases during the growth of a culture under growth permissive conditions and may be referred to as “biomass accumulation” in batch cultures, for example. In continuous or semi-continuous cultures that undergo steady or regular dilution, biomass that is produced that would otherwise accumulate in the culture is removed during culture dilution. Thus, daily biomass productivity (increases in biomass) by these cultures can also be referred to as “biomass accumulation”. Biomass productivity can be assessed as TOC productivity in milligrams per liter (mg/L) per given time period (e.g., per day) and for algae, may be reported as grams per meter² per day (g/m²/day). In the semi-continuous assays provided herein, mg/L values are converted to g/m2/day by taking into account the area of incident irradiance (the SCPA flask rack aperture of 1½″×33/8″, or 0.003145 m²) and the volume of the culture (550 ml). To obtain productivity values in g/m2/day, mg/L values are multiplied by the daily dilution rate (30%) and a conversion factor of 0.175. Where biomass is expressed as a percentage, the percentage is a weight percent unless indicated otherwise.

In the context of the invention, a “nitrogen source” is a source of nitrogen that can be taken up and metabolized by the subject microorganism and incorporated into biomolecules for growth. For example, compounds including nitrogen that cannot be taken up and/or metabolized by the microorganism for growth (e.g., nitrogen-containing biological buffers such as Hepes, Tris, etc.) are not considered nitrogen sources in the context of the invention.

“Reduced nitrogen”, as used herein, is nitrogen in the chemical form of ammonium, ammonia, urea, or an amino acid that can be metabolized by the microorganism being cultured to provide a source of nitrogen for incorporation into biomolecules, thereby supporting growth. For example, in addition to ammonium/ammonia and urea, reduced nitrogen can include various amino acids where the amino acid(s) can serve as a nitrogen source to the subject microorganism. Examples of amino acids can include, without limitation, glutamate, glutamine, histidine, lysine, arginine, asparagine, alanine, and glycine. “Non-reduced nitrogen” in the context of a nitrogen source that can be present in a culture medium for microorganisms refers to nitrate or nitrite that must be reduced prior to assimilation into organic compounds by the microorganism.

“The sole source of nitrogen [in the culture medium]” is used interchangeably with “substantially the sole source of nitrogen” and indicates that no other nitrogen source is intentionally added to the culture medium and/or that no other nitrogen source is present in an amount sufficient to significantly increase the growth of the microorganisms or cells cultured in the referenced medium. Throughout this application, for brevity, the terms “nitrate-only” and “urea-only” are used to characterize culture media in which nitrate is the substantially the sole source of nitrogen that is available to the microorganisms for supporting growth or urea is the only source of nitrogen that is available to the microorganisms for supporting growth, respectively.

Similarly, “the sole source of carbon [in the culture medium]” is used interchangeably with “substantially the sole source of carbon” and indicates that where inorganic carbon is substantially the sole source of carbon in the culture medium no other carbon source is present in an amount sufficient to increase the productivity or growth of the microorganisms or cells cultured in the referenced medium or any other carbon source that may be present is not significantly incorporated into biomolecules such as lipids produced by the microorganisms or cells. “Inorganic carbon” refers to carbon dioxide, carbonate and carbonate salts, and carbonic acid.

Disclosed herein are methods for manipulating, assaying, culturing, and analyzing microorganisms. The invention set forth herein also makes use of standard methods, techniques, and reagents for cell culture, transformation of microorganisms, genetic engineering, and biochemical analysis that are known in the art.

All headings are for the convenience of the reader and do not limit the invention in any way.

Mutant Microorganisms Having Increased Lipid Productivity

The invention provides mutant microorganisms having at least 45% of the biomass productivity of a control microorganism and higher lipid productivity (e.g., higher productivity per day, preferably averaged over the culture period) with respect to the control microorganism when both the mutant microorganism and control microorganism are cultured under identical conditions in which the control microorganism culture is producing biomass. Biomass productivity can be assessed, for example, as ash-free dry weight (AFDW) production or productivity (i.e., amount produced per day) or total organic carbon (TOC) productivity. A mutant microorganism as provided herein can demonstrate greater lipid productivity than a control microorganism and at least 45% of the biomass productivity of the control microorganism over a culture period of at least three days, for example, a culture period of at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least twenty, at least thirty, or at least sixty days when the mutant microorganism and the control microorganism are cultured under conditions that support growth of the control microorganism, i.e., under conditions in which the control microorganism culture produces biomass. In some examples the culture period in which a mutant microorganism as provided herein produces at least 45% of the biomass and produces more lipid with respect to a control microorganism can be less than 180 days, less than 120 days, or less than 90 days. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism under culture conditions in which both the mutant and control microorganism are producing biomass and the mutant produces at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 105%, at least 110%, or at least 120% of the biomass produced by a control microorganism on a daily basis. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism and at least 45% of the biomass but less than 300% or less than 325%, or less than 200% of the biomass produced by the control microorganism. In some examples, a mutant microorganism as provided herein produces higher amounts of lipid with respect to a control microorganism under culture conditions in which both the mutant and control microorganism are producing biomass and actively dividing.

Methods of measuring the amount of lipid produced by microorganisms are well-known in the art and provided in the examples herein. Total extractable lipid can be determined according to Folch et al. (1957) J. Biol. Chem. 226: 497-509; Bligh & Dyer (1959) Can. J. Biochem. Physiol. 37: 911-917; or Matyash et al. (2008) J. Lipid Res. 49:1137-1146, for example, and the percentage of biomass present as lipid can also be assessed using Fourier transform infrared spectroscopy (FT-IR) (Pistorius et al. (2008) Biotechnol & Bioengin. 103:123-129). Additional references for gravimetric analysis of FAME and TAGs are provided in U.S. Pat. No. 8,207,363 and WO 2011127118 for example, each incorporated herein by reference in its entirety. FAME analysis methods can also be found for example as American Oil Chemists' Society Methods Ce 1b-89 and Ce 1-62 (aocs.org/Methods/).

Biomass can be assessed by measuring total organic carbon (TOC) or by other methods, such as measuring ash-free dry weight (AFDW). Methods for measuring TOC are known in the art (e.g., U.S. Pat. No. 8,835,149) and are provided herein. Methods of measuring AFDW are also well-known and can be found, for example, in U.S. Pat. No. 8,940,508, incorporated herein by reference in its entirety.

A mutant microorganism can produce, for example, at least 25% more lipid than a control microorganism and at least 45% as much biomass as the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days during which both the mutant and control microorganisms produce biomass. For example, the average daily lipid productivity can be at least 25% greater than the average daily lipid productivity of a control microorganism and the average daily biomass productivity can be at least 45% as much as the biomass productivity of the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days. In additional examples, a mutant microorganism can produce at least about 50% more lipid than is produced by a control microorganism and at least 45% as much biomass as the control microorganism, i.e., can exhibit no more than a 55% reduction in biomass with respect to the control microorganism, under conditions in which the control microorganism is producing biomass. A mutant can in some examples produce less than 400% or less than 300% more lipid than a control microorganism while accumulating at least 45% as much biomass as the control microorganism during a culture period of at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days.

The culture conditions under which a mutant as provided herein produces at least 25% or at least about 50% more FAME while producing at least 50% of the amount of TOC as a control microorganism can be nutrient replete, and can be nitrogen replete with respect to the control microorganism, that is, the culture conditions can be sufficient in nutrients with respect to the control microorganism such that additional nutrients do not increase the growth rate of the microorganism (where all other culture conditions and ingredients remain the same). For example, the culture conditions can be sufficient in nitrogen with respect to the control microorganism such that additional nitrogen do not increase the growth rate of the microorganism (where all other culture conditions and ingredients remain the same). Alternatively, in some embodiments the culture conditions under which a mutant as provided herein produces at least 25% or at least 50% more FAME (which can be the average daily FAME productivity) while producing at least 45% of the amount of TOC (e.g., the average daily TOC productivity) as a control microorganism can include nitrogen that supports biomass production, but at a lower rate than fully nitrogen replete culture media. For example, the culture conditions may allow for biomass (TOC or AFDW) production at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% the rate of biomass production in fully nitrogen replete culture media.

Mutant microorganisms disclosed herein can produce at least 25% more lipid, e.g., 25% more FAME, as is produced by a control microorganism, while producing at least 45% of the biomass of the control microorganism under conditions that support biomass production that is comparable to the levels of biomass of the control microorganism under nitrogen-replete conditions. For example, biomass production of the control microorganism can be within 20% or within 15% of the biomass production of the control microorganism under nitrogen-replete conditions. Alternatively or in addition, a mutant as provided herein can produce at least 45% of the biomass of the control microorganism while producing at least 25% more lipid than the control microorganism, where the mutant and control microorganism are cultured under conditions that are nitrogen replete with respect to the control microorganism. In various examples, the mutant can produce at least 45% of the biomass produced by a control cell and at least 25% more lipid than the control cell over the same time period in a culture that includes one or more of nitrate or urea, and in some examples can further optionally include less than about 5 mM ammonium, such as less than about 2.5 mM, ammonium, less than about 2 mM ammonium, less than about 1.5 mM ammonium, ammonium, less than about 1 mM ammonium, about 0.5 mM ammonium, or less than 0.5 mM ammonium.

In particular nonlimiting examples, a microorganism can be an algal or heterokont microorganism and can produce at least 25% more FAME while producing at least 45% of the amount of TOC as is produced by a control algal or heterokont microorganism in a culture medium that includes less than about 5 mM, less than about 4.5 mM, less than about 4 mM, less than about 3.5 mM, less than about 3 mM, less than about 2.5 mM, less than about 1 mM, or less than about 0.5 mM ammonium. For example, the ammonium concentration may be at a concentration ranging from about 0 to about 5 mM, from about 0 to about 4.0 mM, from about 0 to about 3 mM, from about 0 to about 2.5 mM, from about 0 to about 2.0 mM, from about 0 to about 1.5 mM, from about 0 to about 1.0 mM, or from about 0 to about 0.5 mM. The ammonium concentration may be at a concentration ranging from about from about 0.5 to about 5 mM, from about 0.5 to about 4 mM, from about 0.5 to about 3 mM, 0.5 to about 2.5 mM, from about 0.5 to about 2.0 mM, from about 0.5 to about 1.5 mM, about 0.5 to about 1 mM, or from about 1 to about 5 mM, about 1 to about 2.5 mM, or from about 0.1 to about 1 mM, from about 0.1 to about 1.5 mM, or from about 0.1 to about 2 mM. In further examples, the ammonium concentration may be at a concentration ranging from about 1 mM to about 2.5 mM or from about 0.2 to about 1.5 mM.

In some examples, a mutant microorganism can be an algal or heterokont cell that produces at least 25% more FAME while producing at least 45% of the amount of TOC as a control microorganism in a culture medium that includes about 2.5 mM ammonium or less, about 2.0 mM ammonium or less, about 1.5 mM ammonium or less, about 1.0 mM ammonium or less, about 0.5 mM ammonium or less, or substantially no ammonium, and can optionally include, for example, at least 1.0 mM, at least 2.0 mM, at least 3.0 mM, at least 4.0 mM, at least 5.0 mM, at least 6.0 mM, at least 7.0 mM, at least 8.0 mM, or at least 10.0 mM nitrate and/or urea. In further nonlimiting examples, a microorganism can be an algal or heterokont cell and can produce at least 50% more FAME while producing at least 45% of the amount of TOC as a control microorganism on a culture medium that includes less than about 5 mM, less than about 2.5 mM, less than about 1 mM, or less than about 0.5 mM ammonium. For example, a microorganism can be an algal or heterokont cell that produces at least 50% more FAME while producing at least 45% of the amount of TOC as a control microorganism in a culture medium that includes about 2.5 mM ammonium or less, about 1.0 mM ammonium or less, about 0.5 mM ammonium or less, or substantially no ammonium, and can include, for example, at least 1.0 mM, at least 2.0 mM, at least 3.0 mM, at least 4.0 mM, at least 5.0 mM, at least 6.0 mM, at least 7.0 mM, at least 8.0 mM, or at least 10.0 mM nitrate and/or urea.

The mutant microorganisms provided herein can have greater partitioning of carbon to lipid with respect to a control microorganism cultured under identical conditions in which both the control microorganism and the mutant microorganism are producing biomass. A mutant having increased partitioning of carbon to lipid with respect to a control microorganism can have increased partitioning of carbon to total extractable lipid, to total neutral lipids, to triglycerides, and/or to FAME-derivatizable lipids. For example, a mutant microorganism as provided herein can have a ratio of the amount of FAME-derivatizable lipids (“FAME”) produced to biomass (TOC or ash-free dry weight (AFDW), for example) produced that is at least 50% higher than that of a control microorganism. Lipid and biomass production and/or production can be assessed, for example, by gravimetric analysis as known in the art and demonstrated in the examples herein. For example, a mutant microorganism as provided herein can have a ratio of FAME to TOC that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which both the culture of the mutant microorganism and the culture of the control microorganism produce biomass. In some example, the FAME/TOC ratio of a mutant microorganism as provided herein can be increased with respect to the FAME/TOC ratio of a control microorganism cultured under identical conditions by less than about 300%.

In various examples a mutant microorganism as provided herein can have a ratio of the amount of FAME produced to TOC produced that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which the control culture produces biomass (e.g., TOC) and the mutant culture produces at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the amount of biomass that is produced by the control culture. In various examples, the FAME/TOC ratio of a mutant as provided herein can be at least 0.30, at least 0.35, at least 0.40, at least 0.45, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.7, or at least 0.75 when cultured under conditions in which the mutant microorganism culture produces at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, or at least 95% as much biomass (e.g., TOC) as a control microorganism culture, under conditions where both the control and mutant cultures produce biomass. In various examples, the FAME/TOC ratio of a mutant as provided herein can be at least 0.30, at least 0.35, at least 0.40, at least 0.45, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.7, or at least 0.75 when cultured under conditions in which the mutant culture produces at least about 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, or at least 100% as much biomass (e.g., TOC) as a control microorganism produces when cultured under nitrogen replete conditions.

In some examples, a mutant microorganism as provided herein can produce at least 50% more FAME while producing at least 80%, at least 85%, or at least 90% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both the control and mutant microorganism produce biomass, and the FAME/TOC ratio of the mutant microorganism is at least 40%, at least 50%, at least 60%, at least 70%, or at least 75% higher than the FAME/TOC of the control microorganism. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.30, at least 0.35, or at least 0.40. The culture conditions can include, for example, a culture medium that includes less than 5 mM, less than 2.5 mM, less than 2 mM, less than 1.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate. In additional examples a mutant microorganism as provided herein can produce at least 60%, at least 70%, or at least 80% more FAME while producing at least 85%, at least 90%, or at least 95% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both wild type and mutant microorganism are producing biomass, and the FAME/TOC ratio of the mutant microorganism is at least 50%, at least 60%, at least 70%, or at least 75% greater than the FAME/TOC ratio of the control microorganism. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.35, at least 0.40, or at least 0.45. The culture conditions can include, for example, a culture medium that includes less than 2.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate. The culture conditions can in some examples include substantially no ammonium, and in some examples can include substantially no reduced nitrogen as a nitrogen source.

In yet further examples a mutant microorganism as provided herein can produce at least 85%, at least 90%, at least 95%, at least 100%, at least 105%, at least 110%, or at least 115% more FAME while producing at least 70%, at least 75%, at least 80%, or at least 85% of the TOC produced by a control cell (such as a wild type cell) when cultured under conditions in which both wild type and mutant microorganism are producing biomass, and the FAME/TOC ratio of the mutant microorganism is at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, or at least 180% greater than the FAME/TOC ratio of the control microorganism. FAME and TOC production can be assessed as average daily FAME productivity over the culture period, for example over a culture period of at least three, at least five, at least ten, at least twenty, at least thirty, or at least sixty days, or a culture period of between three and sixty days, or between three and thirty days, for example between three and fifteen days or between five and fifteen days. The FAME/TOC ratio of the mutant microorganism can be, for example, at least 0.50, at least 0.55, at least 0.60, at least 0.65, at least 0.70, or at least 0.75. The culture conditions can include, for example, a culture medium that includes less than 2.5 mM, less than 1.0 mM, or less than 0.5 mM ammonium and can include at least 2 mM, at least 4 mM, or at least 6 mM urea or nitrate.

In additional examples, a mutant microorganism can produce at least about 70% of the biomass produced by a wild type or control microorganism and at least 90% more lipid than is produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions. FAME and TOC production can be assessed as average daily FAME productivity over the culture period, for example over a culture period of at least three, at least five, at least ten, at least twenty, at least thirty, or at least sixty days. For example the wild type and control microorganism can be cultured in batch, semi-continuous, or continuous culture for at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, twenty, thirty, or sixty days. In some examples the concentration of ammonium in the culture medium may be less than about 5 mM or less than about 2.5 mM. In some examples the culture medium may include at least 2 mM nitrate or at least 2 mM urea. The mutant microorganism can produce, in some examples, at least about 75% or at least about 80% of the biomass produced by a wild type or control microorganism and at least 100% or at least 110% more lipid than is produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions. The FAME/TOC ratio can be at least 80%, at least 100%, at least 120%, or at least 150% greater than the FAME/TOC ratio of a wild type microorganism cultured under the same conditions. In some examples, the mutant microorganism can produce at least about 70% or at least about 75% of the biomass produced by a wild type or control microorganism and at least 100% or at least 120% more FAME lipids than are produced by a wild type or control microorganism when the mutant microorganism and wild type or control microorganism are cultured under the same conditions, and the mutant microorganism can have a FAME/TOC ratio at least 100% or at least 120% greater than the FAME/TOC ratio of a wild type microorganism cultured under the same conditions.

In various embodiments, a mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 125%, or at least 130% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism. In some embodiments the C:N ratio of a mutant as provided herein is between about 7 and about 20 or between about 8 and about 17, or between about 10 and about 15 during the culturing in which mutant produces at least 50% more lipid that a control microorganism while producing at least 50% as much biomass as the control microorganism. A control microorganism in any of the embodiments or examples herein can be a wild type microorganism.

Alternatively or in addition, mutant microorganism as provided herein, e.g., a mutant microorganism such as any described herein that produces at least about 50% of the biomass and at least about 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, or at least 120% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have reduced protein content when compared with a control microorganism. For example, in some embodiments a mutant microorganism as provided herein can have a decrease in protein content of at least 10%, at least 20%, at least 30%, at least 40%, at least 45%, or at least 50% with respect to a control microorganism.

In various embodiments, a mutant microorganism as provided herein can have attenuated expression of a gene encoding a protein whose expression affects the expression of other genes, e.g., at least ten, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 additional genes. For example, a mutant as provided herein can have at least ten genes that are upregulated with respect to a wild type microorganism and at least ten genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (greater lipid production) is expressed. A mutant as provided herein can have at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are upregulated with respect to a wild type microorganism and at least twenty, at least thirty, at least forty, at least fifty, at least sixty, at least seventy, at least eighty, at least ninety, or at least 100 genes that are downregulated with respect to a wild type microorganism under conditions in which the mutant phenotype (e.g., greater lipid production with respect to the wild type microorganism) is expressed. In some embodiments, genes encoding polypeptides involved in protein synthesis can be upregulated in a mutant as provided herein, for example, genes encoding ribosomal polypeptides or other polypeptides that function in translation, including, without limitation, those belonging to gene ontology (GO) groups such as “translation”, “ribosome”, “structural constituent of ribosome”, “eukaryotic translation initiation factor 3 complex”, “translation initiation factor activity”, “translational initiation”, “small ribosomal subunit”, “formation of translation preinitiation complex”, regulation of translation initiation, “eukaryotic 43S preinitiation complex”, and “eukaryotic 48S preinitiation complex”. Alternatively or in combination with the upregulation of genes encoding polypeptides relating to protein synthesis, any of various genes encoding polypeptides involved in nitrogen assimilation such as a molybdenum cofactor biosynthesis protein, a nitrate transporter, a nitrate reductase, a nitrite reductase, a glutamate synthase, a glutamine synthase, a glutamate dehydrogenase, and an ammonium transporter can be downregulated in a mutant as provided herein.

Alternatively or in combination with any of the above, a mutant as provided herein can exhibit upregulation of certain genes related to lipid biosynthesis including but not limited to a lipid droplet surface protein and/or one or more desaturases, elongases, lipases, acyltransferases, and/or glyceraldehyde-3-phosphate dehydrogenases.

The properties of a mutant as provided herein having increased lipid production are compared to the same properties of a control microorganism that may be a wild type organism of the same species as the mutant, preferably the progenitor strain of the lipid-overproducing mutant. Alternatively, a control microorganism can be a microorganism that is substantially identical to the mutant microorganism with the exception that the control microorganism does not have the mutation that leads to higher lipid productivity. For example, a control microorganism can be a genetically engineered microorganism or classically mutated organism that has been further mutated or engineered to generate a mutant having increased lipid productivity and/or increased lipid partitioning as disclosed herein.

In some examples, a control microorganism can be a microorganism that is substantially identical to the mutant microorganism, with the exception that the control microorganism does not have a mutation in a gene or attenuated expression of a gene that regulates lipid induction (i.e., the gene whose mutation results in increased lipid production under conditions in which the mutant microorganism has at least about half the biomass productivity of the progenitor strain). The properties of a lipid-overproducing mutant having a disrupted, attenuated, or otherwise directly or indirectly genetically manipulated gene (resulting in altered structure or expression of the lipid induction regulator gene) are also be compared with the same properties of a control cell that does not have a disrupted, attenuated, or otherwise directly or indirectly genetically manipulated lipid induction regulator gene resulting in altered structure or expression of the lipid induction regulator gene (regardless of whether the cell is “wild-type”). For example, a control cell may be a recombinant cell or a cell mutated in a gene other than the lipid induction regulator gene whose effects are being assessed, etc.

Heterokont species considered for use in the invention include, but are not limited to, Bacillariophytes, Eustigmatophytes, Labrinthulids, and Thraustochytrids, such as, for example, species of Labryinthula, Labryinthuloides, Thraustochytrium, Schizochytrium, Aplanochytrium, Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys, or Ulkenia.

Mutant microorganisms having the properties disclosed herein, such as mutant microorganisms having attenuated expression of a gene that regulates lipid biosynthesis, such as the ZnCys-2845 gene of N. gaditana and orthologs thereof can be, in various examples, of any eukaryotic microalgal strain such as, for example, any species of any of the genera Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox. Non-limiting examples of particularly suitable species include, for instance, heterokont algae, such as but not limited to diatoms such as, for example, a species of any of the genera Amphora, Chaetoceros, Cyclotella, Fragilaria, Fragilaropsis, Hantzschia, Navicula, Nitzschia, Phceodactylum, or Thalassiosira, or Eustigmatophytes, e.g., Chloridella, Chlorobptrys, Ellipsoidion, Eustigmatos, Goniochloris, Monodopsis, Monodus, Nannochloropsis, Pseudocharaciopsis, Pseudostaruastrum, Pseudotetraëdriella, or Vischeria. In some examples, the mutant alga cell is a species of Ellipsoidion, Eustigmatos, Monodus, Nannochloropsis, Pseudostaruastrum, Pseudotetraëdriella, or Vischeria. In some examples, the mutant alga cell is a species of Nannochloropsis, e.g., N. gaditana, N. granulata, N. limnetica N. oceanica, N oculata, or N. salina.

The mutants can be spontaneous mutants, classically-derived mutants, or engineered mutants having attenuated expression of a regulator gene. For example, a mutant microorganism such as any described herein can be a mutant obtained by classical mutagenesis or genetic engineering. In particular embodiments, a mutant microorganism as provided herein is a genetically engineered mutant, for example, a microorganism into which at least one exogenous nucleic acid molecule has been introduced, e.g., into which at least one recombinant nucleic acid molecule has been introduced, where the mutant microorganism is genetically engineered to include the exogenous nucleic acid molecule and/or the exogenous nucleic acid molecule effects at least one alteration of the microorganism's genome.

In various examples, the mutant microorganism is an algal or heterokont species and has attenuated expression of a gene that encodes a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 and/or has a coding region having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity SEQ ID NO: 1 or any of SEQ ID NOs:72-84. Alternatively or in addition, the mutant microorganism is an algal or heterokont species and has attenuated expression of a gene that encodes a polypeptide having an amino acid sequence with at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to amino acids 1-200 of SEQ ID NO:20 or to SEQ ID NO:18 or SEQ ID NO: 19. The mutant microorganism can in certain embodiments further include a domain having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25. The domain can be a PAS3 domain. The mutant microorganism can be engineered to attenuate expression of at least one gene encoding a polypeptide as set forth herein by any gene attenuation method, such as any disclosed herein or equivalents thereof.

The polypeptide encoded by the gene whose expression is attenuated can be a transcription factor protein of the Zn(II)2Cys6 fungal-type DNA-binding domain protein family. The polypeptide encoded by the gene whose expression is attenuated can include a Zn(2)Cys(6) domain, categorized as conserved domain cd00067 by the NCBI conserved domain database (ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), referred to as the “GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain” that is found in transcription factors such as GAL4, also characterized as smart00066: “GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain”. This domain, which may be referred to herein as a Zn2Cys6, Zn₂Cys₆, or Zn(2)Cys(6) domain or simply a ZnCys domain, occurs at amino acids 190-219 of SEQ ID NO:2, is also characterized as pfam PF00172 (“Zn_Clus” or “Fungal Zn(2)-Cys(6) binuclear cluster domain”) with a gathering cutoff for this family of 20.8. In some embodiments, a mutant as provided herein can have attenuated expression of a gene encoding a polypeptide having a Zn(2)Cys(6) domain having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3.

Alternatively or in addition, the gene whose expression is attenuated can encode a polypeptide having a PAS_3 domain (pfam 08447, having a gathering cutoff of 25.6) also called “PAS fold domain” or simply a PAS domain, such as, for example, a PAS domain having at least at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25.

The mutant microorganism having attenuated expression of a gene that regulates lipid production can be a “knockout” mutant, for example, in which the reading frame of the polypeptide is disrupted such that a functional protein is not produced. For example, the gene can include an insertion, deletion, or mutation in the reading frame that results in no functional protein being made. The insertion, deletion, or mutation can be made by various means, such as, for example, homologous recombination constructs, RNA-guided endonucleases that employ guide RNAs, optionally in combination with donor DNA fragments, etc. In other examples, the mutant microorganism can be a “knockdown” mutant in which expression of the gene is reduced with respect to a wild type cell. For example, transcript levels of the target gene, which may be, for example, a gene encoding a Zn(2)-C6 fungal-type DNA-binding domain protein, can be reduced between about 5% and about 95% or between about 10% and about 90% with respect to the transcript level in a control microorganism, such as a wild type microorganism. Knockdowns can be mutants in which a mutation, insertion, or deletion occurs in a non-coding region of the gene or can be effected by expressing constructs in the cells that reduce expression of the targeted gene, such as ribozyme, RNAi, or antisense constructs. In some embodiments gene attenuation can be effected by insertion of a DNA fragment into a noncoding region of the gene, such as a 5′UTR or 3′ UTR. Insertion of a DNA fragment can optionally be by use of an RNA-guided endonuclease, e.g., a cas protein. The mutant microorganism having attenuated expression of a gene that regulates lipid production can include, for example, one or more of an RNAi construct for expressing RNAi or one or more RNAi molecules, an antisense construct for expressing antisense RNA or one or more antisense molecules, a ribozyme construct for expressing a ribozyme or one or more ribozymes, one or more guide RNAs, one or more constructs for expressing a guide RNA, one or more donor fragments for cas-mediated insertion, one or more homologous recombination constructs, one or more genes encoding a cas enzyme, or a cas enzyme, one or more genes encoding a TALEN, or one or more TALENs, or one or more meganucleases.

Thus, provided herein are microorganisms that have attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family, i.e., a polypeptide that includes a “GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain” (NCBI conserved domain cd00067) and/or recruits to pfam PF00172 (“Zn_Clus” or “Fungal Zn(2)-Cys(6) binuclear cluster domain”) with a bit score greater than the gathering cutoff for this family of 20.8. Alternatively or in addition a mutant microorganism as provided herein may have attenuated expression of a gene encoding a polypeptide that includes a PAS domain (e.g., a “PAS3 domain” or “PAS fold domain”) that may be characterized as PF08447 or PF00989. The mutant can produce more lipid that a control microorganism under culture conditions in which both the mutant and the control microorganism produce biomass and in which the mutant microorganism produces at least 50% of the biomass as is produced by the control microorganism. For example, the mutant microorganism can produce at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 110% or at least 120% more lipid that a control microorganism under culture conditions in which both the mutant and the control microorganism produce biomass and in which the mutant microorganism produces at least 50% of the biomass as is produced by the control microorganism. In various embodiments the microorganism that has attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family and/or having a PAS domain produces at least 50% more the lipid and at least 50% of the biomass as is produced by a control microorganism on a daily basis for at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, or at least twelve-days of culturing. The mutant can include any of the properties described hereinabove, including, without limitation, increased FAME/TOC ratio under conditions in which the mutant produces more lipid that a control microorganism. The culture conditions under which the mutant produces a higher amount of lipid while producing at least 50% of the biomass as control microorganism can include less than 2.5 mM, less than 1.5 mM, less than 1 mM, or about 0.5 mM or less ammonium. The culture conditions under which the mutant produces a higher amount of lipid while producing at least 50% of the biomass as control microorganism can include a culture medium that includes nitrate, such as at least 2, 3, 4, or 5 mM nitrate. Alternatively or in addition, the culture conditions can include a culture medium that includes urea, such as at least 2, 3, 4, or 5 mM urea. The culture in some examples can provide nitrate as substantially the sole source of nitrogen available to the mutant and control microorganism. The control microorganism can be a wild type microorganism of the same species as the mutant, e.g., can be a wild type strain from which the mutant was derived. The microorganism can be an alga or a heterokont, and in some examples is a heterokont alga such as, but not limited to, a diatom or eustigmatophyte. In various examples lipid can be measured as FAME lipids, and biomass can be measured as, for example, TOC.

Alternatively or in addition, a mutant microorganism as provided herein having attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family can demonstrate a FAME/TOC ratio that is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85, at least 90%, at least 95%, at least 100%, at least 110%, at least 120%, at least 130%, at least 140%, at least 150%, at least 160%, at least 170%, at least 180%, at least 190%, at least 200%, or at least 250% higher than the FAME/TOC ratio of a control microorganism when both the mutant microorganism and the control microorganism are cultured under conditions in which the control culture produces biomass (e.g., TOC) and the mutant culture produces at least 45%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the amount of biomass that is produced by the control culture. In an exemplary embodiment, a ZnCys attenuation strain can exhibit about twice the lipid productivity of a control strain (e.g., a wild type strain), while allocating approximately 35-70% of its carbon to lipid, for example, while allocating from about 40% to about 65% of its carbon to lipid, such as about 45%, 50%, 60%, or 65% of its carbon to lipid in a semicontinuous or continuous culture system. Further additionally or alternatively, a mutant microorganism as provided herein, e.g., a mutant microorganism having attenuated expression of a gene encoding a polypeptide of the Zn(II)2Cys6 family that produces at least about 50% of the biomass and at least about 50% more lipid than is produced by a control microorganism cultured under the same conditions, where the conditions support daily biomass accumulation by the control microorganism, can have a higher carbon to nitrogen (C:N) ratio than a control microorganism. For example, the C:N ratio can be from about 1.5 to about 2.5 the C:N ratio of a control microorganism when the mutant microorganism and the control microorganism are cultured under conditions in which both the mutant and the control microorganisms accumulate biomass, and the mutant produces at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% more lipid that the control microorganism and at least 50%, at least 60%, at least 70%, at least 80%, or at least 85% of the TOC of the control microorganism.

The gene whose expression is attenuated in a mutant that has higher lipid productivity than a control microorganism can be a gene encoding a polypeptide of the Zn(II)2Cys6 family that has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, or SEQ ID NO: 18. Alternatively or in addition, the gene whose expression is attenuated can encode a polypeptide having a PAS3 domain (pfam08447), such as, for example, a PAS3 domain having at least at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25.

A mutant microorganism as provided herein can be designed by targeting an endogenous gene of a microorganism of interest that encodes a polypeptide that includes a Zn2Cys6 domain as disclosed herein and/or a PAS3 domain as disclosed herein. Such genes can be identified in a microorganism of interest by bioinformatics methods, molecular biology techniques and combinations thereof. For example, a gene encoding a polypeptide that includes a Zn2Cys6 domain and/or a PAS3 domain can be identified using Southern hybridization, screening of cDNA libraries by hybridization or PCR, for example, using degenerate probes and/or primers. Genome sequences available in public or proprietary databases can be searched by any of a number of programs that perform sequence matching (blast programs) or analyze domain structures of encoded amino acid sequences. For example, hmmer.org provides software for analyzing structural and functional domains encoded by genes that can be used to scan genome sequences, including, for example, hmmsearch and hmmscan. Such searches can be done online. Programs such as MUSCLE and hmmalign can also be used to search for orthologs of proteins such as the proteins disclosed herein (e.g., ZnCys-2845 and orthologs) by constructing phylogenetic trees to determine relationships among proteins. In addition, sequence-based searches, including blastp, blastn, and tblastn (protein sequence queried against translated nucleotide sequence). Gene targeting can make use of the obtained sequences from the genome of the microorganism of interest. It is not necessary to resolve the complete structure of a gene to target the gene for attenuation. For example, using methods disclosed herein, including, without limitation, cas/CRISPR genome editing, RNAi constructs, antisense constructs, homologous recombination constructs, and ribozyme constructs, only a portion of a gene sequence can be employed in gene attenuation constructs and techniques.

Gene Attenuation

A mutant microorganism having attenuated expression of a gene that regulates lipid biosynthesis can be a mutant generated by any feasible method, including but not limited to UV irradiation, gamma irradiation, or chemical mutagenesis, and screening for mutants having increase lipid production, for example using the assays disclosed herein or by staining with lipophilic dyes such as Nile Red or BODIPY (e.g., Cabanelas et al. (2015) Bioresource Technology 184:47-52). Methods for generating mutants of microbial strains are well-known.

A mutant as provided herein that produces at least 25% more lipid while producing at least 50% of the biomass as the progenitor cell can also be a genetically engineered mutant, for example, a mutant in which a regulatory gene such as Zn(2)-C(6) fungal-type DNA-binding domain protein (e.g., ZnCys-2845 or an ortholog thereof, e.g., a gene encoding a polypeptide having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or any of SEQ ID NOs:5-18) has been targeted by homologous recombination for knock-out or gene replacement (for example with mutated form of the gene that encodes a polypeptide having reduced activity with respect to the wild type polypeptide). For example, a microbial strain of interest may be engineered by site directed homologous recombination to insert a sequence into a genomic locus and thereby alter a gene and/or its expression, where the insertion can be, as nonlimiting examples, in the coding region of the gene, in an intron of the gene, in the 3′ UTR or the gene, in the 5′ UTR of the gene, or upstream of the transcriptional start site, i.e., in the promoter region of the gene.

For example, gene knockout or replacement by homologous recombination can be by transformation of a homologous recombination nucleic acid construct, i.e., a nucleic acid (e.g., DNA) fragment that includes a sequence homologous to the region of the genome to be altered, where the homologous sequence is interrupted by a foreign sequence, typically but not necessarily by a selectable marker gene that allows selection for the integrated construct. The genome-homologous flanking sequences on either side of the foreign sequence or mutated gene sequence can be for example, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1,000, at least 1,200, at least 1,500, at least 1,750, or at least 2,000 nucleotides in length. A gene knockout or gene “knock in” construct in which a foreign sequence is flanked by target gene sequences, can be provided in a vector that can optionally be linearized, for example, by cleavage at a site outside of the region that is to undergo homologous recombination, or can be provided as a linear fragment that is not in the context of a vector, for example, the knock-out or knock-in construct can be an isolated or synthesized fragment, including but not limited to a PCR product. In some instances, a split marker system can be used to generate gene knock-outs by homologous recombination, where two DNA fragments can be introduced that can regenerate a selectable marker and disrupt the gene locus of interest via three crossover events (Jeong et al. (2007) FEMS Microbiol Lett 273: 157-163).

In one aspect the invention provides genetically modified organisms, e.g., microorganisms having one or more genetic modifications for attenuating expression of a lipid regulator gene such as a gene encoding a Zn(2)-C(6) fungal-type DNA-binding domain protein, that additionally may have at least 55% identity to any of SEQ ID NO:2 or SEQ ID NOs:5-18. As used herein “attenuating expression of a lipid regulator gene” means reducing or eliminating expression of the gene in any manner that reduces production of the fully functional lipid regulator protein. As used herein, “lipid regulator gene” refers to a gene whose attenuated expression in an organism or cell results in altered regulation of at least 50, at least 100, at least 200, or at least 300 genes in the organism or cell with respect to a control organism or cell and results in altered lipid productivity by the organism or cell. In an exemplary embodiment, a lipid regulator gene is a gene encoding a Zn(2)-C(6) fungal-type DNA-binding domain protein. Means for attenuating a lipid regulator gene include, for example, homologous recombination constructs; CRISPR systems, including one or more guide RNAs, a cas enzyme such but not limited to a Cas9 enzyme or a gene encoding a cas enzyme, and optionally, one or more donor fragments for insertion into a targeted site; RNAi constructs; shRNAs; antisense RNA constructs; ribozyme constructs; TALENS or genes encoding TALENs, Zinc Finger nucleases or genes encoding Zinc Finger nucleases; and meganucleases or genes encoding Zinc Finger nucleases.

For example, a recombinant microorganism engineered to have attenuated expression of a lipid regulator gene can have a disrupted lipid regulator gene that includes as least one insertion, mutation, or deletion that reduces or abolishes expression of the gene such that a fully functional lipid regulator gene is not produced or is produced in lower amounts than is produced by a control microorganism that does not include a disrupted lipid regulator gene. The disrupted lipid regulator gene can be disrupted by, for example, an insertion or gene replacement mediated by homologous recombination and/or by the activity of a meganuclease, zinc finger nuclease (Perez-Pinera et al. (2012) Curr. Opin. Chem. Biol. 16: 268-277), TALEN (WO 2014/207043; WO 2014/076571), or a cas protein (e.g., a Cas9 protein) of a CRISPR system.

CRISPR systems, reviewed recently by Hsu et al. (Cell 157:1262-1278, 2014) include, in addition to the cas nuclease polypeptide or complex, a targeting RNA, often denoted “crRNA”, that interacts with the genome target site by complementarity with a target site sequence, a trans-activating (“tracr”) RNA that complexes with the cas polypeptide and also includes a region that binds (by complementarity) the targeting crRNA.

The invention contemplates the use of two RNA molecules (a “crRNA” and a “tracrRNA”) that can be co-transformed into a host strain (or expressed in a host strain) that expresses or is transfected with a cas protein for genome editing, or the use of a single guide RNA that includes a sequence complementary to a target sequence as well as a sequence that interacts with a cas protein. That is, in some strategies a CRISPR system as used herein can comprise two separate RNA molecules (a “tracr-RNA” and a “targeter-RNA” or “crRNA”, see below) and referred to herein as a “two RNA molecule CRISPR system” “two RNA guide system” or a “Split guide RNA system”. Alternatively, as illustrated in the examples, the DNA-targeting RNA can also include the trans-activating sequence for interaction with the cas protein (in addition to the target-homologous (“cr”) sequences), that is, the DNA-targeting RNA can be a single RNA molecule and is referred to herein as a “chimeric guide RNA,” a “single-guide RNA,” or an “sgRNA.” The terms “DNA-targeting RNA” and “gRNA” are inclusive, referring both to a two RNA guide system and to single-molecule DNA-targeting RNAs (i.e., sgRNAs). Both single-molecule guide RNAs and two RNA guide systems have been described in detail in the literature and for example, in U.S. Patent Application Publication No. US 2014/0068797, incorporated by reference herein in its entirety, and both are considered herein.

Any cas protein can be used in the methods herein, such as but not limited to, Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof. The cas protein can be a Cas9 protein, such as a Cas9 protein of Staphylococcus pyogenes, S. thermophilus, S. pneumonia, S. aureus, or Neisseria meningitidis, as nonlimiting examples. Also considered are the Cas9 proteins provided as SEQ ID NOs: 1-256 and 795-1346 in U.S. Patent Application Publication No. US 2014/0068797, and chimeric Cas9 proteins that may combine domains from more than one cas9 protein, as well variants and mutants of identified Cas9 proteins. In additional examples, a cas protein used for genome modification can be a Cpf1 protein that uses a single RNA guide system, such as but not limited to a Cpf1 protein of Acidaminococcus or Lachnospiraceae (see for example Fagerlund et al. (2015) Genome Biol. 15:261; Zetsche et al. (2015) Cell 163:1-13); and European patent application EP3009511), as well as the C2c1, C2c2, C2c3 RNA-guided nucleases (Shmakov et al. (2015) Molecular Cell 60:1-13).

Cas nuclease activity cleaves target DNA to produce double strand breaks. These breaks are then repaired by the cell in one of two ways: non-homologous end joining or homology-directed repair. In non-homologous end joining (NHEJ), the double-strand breaks are repaired by direct ligation of the break ends to one another. In this case, no new nucleic acid material is inserted into the site, although some nucleic acid material may be lost, resulting in a deletion, or altered, often resulting in mutation. In homology-directed repair, a donor polynucleotide (sometimes referred to as a “donor DNA” or “editing DNA”) which may have homology to the cleaved target DNA sequence is used as a template for repair of the cleaved target DNA sequence, resulting in the transfer of genetic information from the donor polynucleotide to the target DNA. As such, new nucleic acid material may be inserted/copied into the site. The modifications of the target DNA due to NHEJ and/or homology-directed repair (for example using a donor DNA molecule) can lead to, for example, gene correction, gene replacement, gene tagging, transgene insertion, nucleotide deletion, gene disruption, gene mutation, etc.

In some instances, cleavage of DNA by a site-directed modifying polypeptide (e.g., a cas nuclease, zinc finger nuclease, meganuclease, or TALEN) may be used to delete nucleic acid material from a target DNA sequence by cleaving the target DNA sequence and allowing the cell to repair the sequence in the absence of an exogenously provided donor polynucleotide. Such NHEJ events can result in mutations (“mis-repair”) at the site of rejoining of the cleaved ends that can resulting in gene disruption.

Alternatively, if a DNA-targeting RNA is co-administered to cells that express a cas nuclease along with a donor DNA, the subject methods may be used to add, i.e., insert or replace, nucleic acid material to a target DNA sequence (e.g., “knock out” by insertional mutagenesis, or “knock in” a nucleic acid that encodes a protein (e.g., a selectable marker and/or any protein of interest), an siRNA, an miRNA, etc., to modify a nucleic acid sequence (e.g., introduce a mutation), and the like.

A donor DNA can in particular embodiments include a gene regulatory sequence (e.g., a promoter) that can, using CRISPR targeting, be inserted upstream of the coding regions of the gene and upstream of the presumed proximal promoter region of the gene, for example, at least 50 bp, at least 100 bp, at least 120 bp, at least 150 bp, at least 200 bp, at least 250 bp, at least 300 bp, at least 350 bp, at least 400 bp, at least 450 bp, or at least 500 bp upstream of the initiating ATG of the coding region of the lipid regulator gene. The donor DNA can include a sequence, such as for example a selectable marker or any convenient sequence, that may be interfere with the native promoter. The additional sequence inserted upstream of the initiating ATG of the lipid regulator open reading frame (e.g., in the 5′UTR or upstream of the transcriptional start site of the lipid regulator gene) can decrease or even eliminate expression of the endogenous lipid regulator gene. Alternatively or in addition, the native lipid regulator gene can have its endogenous promoter wholly or partially replaced by a weaker or differently regulated promoter, or a non-promoter sequence.

In some examples, a nucleic acid molecule introduced into a host cell for generating a high efficiency genome editing cell line encodes a cas9 enzyme that is mutated to with respect to the corresponding wild-type enzyme such that the mutated cas9 enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (an enzyme that cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A. In some embodiments, a Cas9 nickase may be used in combination with guide sequence(s), e.g., two guide sequences, which target respectively sense and antisense strands of the DNA target. This combination allows both strands to be nicked and used to induce NHEJ. Two nickase targets (within close proximity but targeting different strands of the DNA) can be used to inducing mutagenic NHEJ. Such targeting of a locus using enzymes that cleave opposite strains at staggered positions can also reduce nontarget cleavage, as both strands must be accurately and specifically cleaved to achieve genome mutation.

In additional examples, a mutant cas9 enzyme that is impaired in its ability to cleave DNA can be expressed in the cell, where one or more guide RNAs that target a sequence upstream of the transcriptional or translational start site of the targeted gene are also introduced. In this case, the cas enzyme may bind the target sequence and block transcription of the targeted gene (Qi et al. (2013) Cell 152:1173-1183). This CRISPR interference of gene expression can be referred to as RNAi and is also described in detail in Larson et al. (2013) Nat. Protoc. 8: 2180-2196.

In some cases, a cas polypeptide such as a Cas9 polypeptide is a fusion polypeptide, comprising, e.g.: i) a Cas9 polypeptide (which can optionally be variant Cas9 polypeptide as described above); and b) a covalently linked heterologous polypeptide (also referred to as a “fusion partner”). A heterologous nucleic acid sequence may be linked to another nucleic acid sequence (e.g., by genetic engineering) to generate a chimeric nucleotide sequence encoding a chimeric polypeptide. In some embodiments, a Cas9 fusion polypeptide is generated by fusing a Cas9 polypeptide with a heterologous sequence that provides for subcellular localization (i.e., the heterologous sequence is a subcellular localization sequence, e.g., a nuclear localization signal (NLS) for targeting to the nucleus; a mitochondrial localization signal for targeting to the mitochondria; a chloroplast localization signal for targeting to a chloroplast; an ER retention signal; and the like). In some embodiments, the heterologous sequence can provide a tag (i.e., the heterologous sequence is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), YFP, RFP, CFP, mCherry, tdTomato, and the like; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like).

Host cells can be genetically engineered (e.g., transduced or transformed or transfected) with, for example, a vector construct that can be, for example, a vector for homologous recombination that includes nucleic acid sequences homologous to a portion of a lipid regulator gene locus of the host cell or to regions adjacent thereto, or can be an expression vector for the expression of any or a combination of: a cas protein (e.g., a cas9 protein), a CRISPR chimeric guide RNA, a crRNA, and/or a tracrRNA, an RNAi construct (e.g., a shRNA), an antisense RNA, or a ribozyme. The vector can be, for example, in the form of a plasmid, a viral particle, a phage, etc. A vector for expression of a polypeptide or RNA for genome editing can also be designed for integration into the host, e.g., by homologous recombination. A vector containing a polynucleotide sequence as described herein, e.g., sequences having homology to host lipid regulator gene sequences (including sequences that are upstream and downstream of the lipid regulator—encoding sequences), as well as, optionally, a selectable marker or reporter gene, can be employed to transform an appropriate host to cause attenuation of a lipid regulator gene.

The recombinant microorganism in some examples can have reduced but not abolished expression of the lipid regulator gene, and the recombinant microorganism can have an increase in lipid production of from about 25% to about 200% or more, for example. A genetically modified microorganism as provided herein can in some examples include a nucleic acid construct for attenuating the expression of a lipid regulator gene, such as, for example, a gene encoding a polypeptide having at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2 or any of SEQ ID NO:5-18. For example, a host microorganism can include a construct for expressing an RNAi molecule, ribozyme, or antisense molecule that reduces expression of a lipid regulator gene encoding a polypeptide having at least 55% identity to SEQ ID NO:2 or any of SEQ ID NO:5-18. In some examples, a recombinant microorganism as provided herein can include at least one introduced (exogenous or non-native) construct for reducing expression of a lipid regulator gene.

In some examples, engineered strains can be selected for expression of a lipid regulator gene that is decreased with respect to a control cell that does not include a genetic modification for attenuating lipid regulator gene expression, but not eliminated, using methods known in the art, such as, for example, RNA-Seq or reverse transcription-PCR (RT-PCR).

A genetically engineered strain as provided herein can be engineered to include a construct for attenuating gene expression by reducing the amount, stability, or translatability of mRNA of a gene encoding a lipid regulator. For example, a microorganism such as an algal or heterokont strain can be transformed with an antisense RNA, RNAi, or ribozyme construct targeting an mRNA of a lipid regulator gene using methods known in the art. For example, an antisense RNA construct that includes all or a portion of the transcribed region of a gene can be introduced into a microorganism to decrease gene expression (Shroda et al. (1999) The Plant Cell 11:1165-78; Ngiam et al. (2000) Appl. Environ. Microbiol. 66: 775-782; Ohnuma et al. (2009) Protoplasma 236: 107-112; Lavaud et al. (2012) PLoS One 7:e36806). Alternatively or in addition, an RNAi construct (for example, a construct encoding a short hairpin RNA) targeting a gene having a Zn(2)Cys(6) domain can be introduced into a microorganism such as an alga or heterokont for reducing expression of the lipid regulator gene (see, for example, Cerruti et al. (2011) Eukaryotic Cell (2011) 10: 1164-1172; Shroda et al. (2006) Curr. Genet. 49:69-84).

Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity. For example, U.S. Pat. No. 5,354,855 reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known ribonucleases and approaching that of the DNA restriction enzymes. Catalytic RNA constructs (ribozymes) can be designed to base pair with an mRNA encoding a gene as provided herein to cleave the mRNA target. In some examples, ribozyme sequences can be integrated within an antisense RNA construct to mediate cleavage of the target. Various types of ribozymes can be considered, their design and use is known in the art and described, for example, in Haseloff et al. (1988) Nature 334:585-591.

Ribozymes are targeted to a given sequence by virtue of annealing to a site by complimentary base pair interactions. Two stretches of homology are required for this targeting. These stretches of homologous sequences flank the catalytic ribozyme structure defined above. Each stretch of homologous sequence can vary in length from 7 to 15 nucleotides. The only requirement for defining the homologous sequences is that, on the target RNA, they are separated by a specific sequence which is the cleavage site. For hammerhead ribozyme, the cleavage site is a dinucleotide sequence on the target RNA is a uracil (U) followed by either an adenine, cytosine or uracil (A,C or U) (Thompson et al., (1995) Nucl Acids Res 23:2250-68). The frequency of this dinucleotide occurring in any given RNA is statistically 3 out of 16. Therefore, for a given target messenger RNA of 1,000 bases, 187 dinucleotide cleavage sites are statistically possible.

The general design and optimization of ribozyme directed RNA cleavage activity has been discussed in detail (Haseloff and Gerlach (1988) Nature 334:585-591; Symons (1992) Ann Rev Biochem 61: 641-71; Chowrira et al. (1994) J Biol Chem 269:25856-64; Thompson et al. (1995) supra), all incorporated by reference in their entireties. Designing and testing ribozymes for efficient cleavage of a target RNA is a process well known to those skilled in the art. Examples of scientific methods for designing and testing ribozymes are described by Chowrira et al., (1994) supra and Lieber and Strauss (1995) Mol Cell Biol. 15: 540-51, each incorporated by reference. The identification of operative and preferred sequences for use in down regulating a given gene is a matter of preparing and testing a given sequence, and is a routinely practiced “screening” method known to those of skill in the art.

The use of RNAi constructs is described in literature cited above as well as in US2005/0166289 and WO 2013/016267, for example. A double stranded RNA with homology to the target gene is delivered to the cell or produced in the cell by expression of an RNAi construct, for example, an RNAi short hairpin (sh) construct. The construct can include a sequence that is identical to the target gene, or at least 70%, 80%, 90%, 95%, or between 95% and 100% identical to a sequence of the target gene. The construct can have at least 20, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, or at least 1 kb of sequence homologous to the target gene. Expression vectors can be engineered using promoters selected for continuous or inducible expression of an RNAi construct, such as a construct that produces an shRNA.

A nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80% identity, such as at least 85%, at least 90%, at least 95%, or at least 99% or complementarity to at least a portion of the sequence of an endogenous lipid regulator gene of the microorganism to be engineered. A nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80%, such as at least 95% or about 100%, identity or complementarity to the sequence of a naturally-occurring gene, such as a gene having encoding a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80% or at least 85%, at least 90%, or at least 95% sequence identity to an endogenous lipid regulator gene. For example, a nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, or at least sixty nucleotides having at least 80% identity or complementarity to the sequence of a naturally-occurring lipid regulator gene, such as any provided herein. The nucleotide sequence can be, for example, from about 30 nucleotides to about 3 kilobases or greater, for example, from 30-50 nucleotides in length, from 50 to 100 nucleotides in length, from 100 to 500 nucleotides in length, from 500 nucleotides to 1 kb in length, from 1 kb to 2 kb in length, or from 2 to 5 kb. For example, an antisense sequence can be from about 100 nucleotides to about 1 kb in length. For example, a nucleic acid construct for gene attenuation, e.g., a ribozyme, RNAi, or antisense construct can include at least fifteen, at least twenty, at least thirty, at least forty, at least fifty, at least sixty, or at least 100 nucleotides having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, or at least 85%, for example at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, or at least 95% identity or complementarity to an endogenous lipid regulator gene or a portion thereof.

Promoters used in antisense, RNAi, or ribozyme constructs can be any that are functional in the host organism and that are suitable for the levels of expression required for reducing expression of the target gene to a desired amount. Promoters functional in algae and heterokonts are known in the art and disclosed herein. The construct can be transformed into algae using any feasible method, include any disclosed herein. A recombinant organism or microorganism transformed with a nucleic acid molecule for attenuating lipid regulator gene expression, such as but not limited to an antisense, RNAi, or ribozyme construct, can have the properties of a lipid regulator mutant as described herein, including, for example, reduced chlorophyll, increased photosynthetic efficiency, and increased productivity in culture, with respect to a host organism or microorganism that does not include the exogenous nucleic acid molecule that results in attenuated gene expression.

In additional examples, such as disclosed in Examples herein, gene attenuation that decreases but does not eliminate expression of the target gene can be achieved through the use of homologous recombination or CRISPR/Cas9 genome editing where the donor fragment is targeted for insertion into a non-coding region of a gene. For example, a selectable marker cassette or other donor fragment can be targeted by the use of an appropriate guide RNA to the 5′ UTR, 3′ UTR, or an intron of a gene whose reduced expression is desired. Thus, another aspect of the invention is a method for attenuating expression of a gene the includes inserting a nucleic acid fragment into a site upstream of the translational start site or downstream of a translational termination site, wherein the expression level of the gene is reduced. As nonlimiting examples, a donor fragment insertion can be introduced into a region up to 2 kb upstream of the translational start site of a gene, or up to 2 kb downstream of the termination codon of a gene. For example, an insertion that is targeted to a site of between about 5 bp and 2 kb upstream of the translational start site, or between about 10 bp and 1.5 kb upstream of the translational start site, or between about 10 bp and about 1.2 kb upstream of the translational start site, or between about 20 bp and about 1 kb upstream of the translational start site. Alternatively or in addition, an insertion can be targeted to the 3′ UTR of a gene. Alternatively or in addition, an insertion that is targeted to a site of between about 5 bp and 2 kb downstream of the translational termination site (stop codon), or between about 10 bp and 1.5 kb downstream of the stop codon, or between about 10 bp and about 1.2 kb downstream of the stop codon, or between about 20 bp and about 1 kb downstream of the stop codon. Without being limited to any particular mechanism, such insertions may reduce the rate or transcription of a gene or may reduce the stability of a resulting transcript.

Nucleic Acid Molecules and Constructs

Also provided herein are nucleic acid molecules encoding polypeptides that include amino acid sequences having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16, or SEQ ID NO: 17. Alternatively or in addition, a nucleic acid molecule as provided herein can include a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84. The polypeptide having at least 60% identity to an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17 or encoded by SEQ ID NO:1 or any of SEQ ID NOs:72-84 can include an amino acid sequence encoding a Zn(2)Cys(6) domain, e.g., a domain belonging to pfam PF00172. For example, the polypeptide encoded by the nucleic acid molecule can include a Zn(2)Cys(6) domain having an amino acid sequence with at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:3. Alternatively or in addition, a polypeptide encoded by a nucleic acid molecule as provided herein can optionally further include a PAS (or PAS3) domain. For example a polypeptide encoded by a nucleic acid molecule as provided herein can include a PAS domain having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NO:21-SEQ ID NO:25.

The nucleic acid molecule in various examples can be or comprise a cDNA that lacks one or more introns present in the naturally-occurring gene, or, alternatively, can include one or more introns not present in the naturally-occurring gene. The nucleic acid molecule in various examples can have a sequence that is not 100% identical to a naturally-occurring gene. For example, the nucleic acid molecule can include a mutation with respect to a naturally-occurring gene that reduces the activity of the encoded polypeptide or reduces expression of the mRNA or protein encoded by the gene.

The nucleic acid molecule in various examples can comprise a heterologous promoter operably linked to the sequence encoding a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 and/or can comprise a heterologous promoter operably linked to a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84. Alternatively or in addition, a nucleic acid molecule can comprise a vector that includes a sequence encoding a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17 and/or has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

A further aspect of the invention is a construct designed for attenuating expression of a gene encoding a Zn(2)Cys(6) DNA-binding domain polypeptide. The construct can be or comprise, in various examples, a sequence encoding a guide RNA of a CRISPR system, an RNAi construct, an antisense construct, a ribozyme construct, or a construct for homologous recombination, e.g., a construct having one or more nucleotide sequences having homology to a naturally-occurring Zn(2)Cys(6) domain-encoding gene as disclosed herein and/or sequences adjacent thereto in the native genome from which the gene is derived. For example, the construct can include at least a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain, e.g., a sequence homologous to at least a portion of an gene that encodes a polypeptide that includes an amino acid sequence having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17 or can include at least a portion of a nucleic acid sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:1 or any of SEQ ID NOs:72-84.

The construct for gene attenuation can include, for example, at least a portion of the coding region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17 or at least a portion of a gene having at least 50% identity to SEQ ID NO: 1 or any of SEQ ID NOs:72-84, at least a portion of an intron of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, at least a portion of a 5′UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, at least a portion of the promoter region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and/or at least a portion of a 3′ UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In some examples, the construct can be an RNAi, ribozyme, or antisense construct and can include a sequence from the transcribed region of the gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17 in either sense or antisense orientation.

In further examples a construct can be designed for the in vitro or in vivo expression of a guide RNA (e.g., of a CRISPR system) designed to target a gene having a sequence having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least a portion of SEQ ID NO: 1 or any of SEQ ID NOs:72-84 or coding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and can include a sequence homologous to a portion of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, including, for example, an intron, a 5′UTR, a promoter region, and/or a 3′ UTR of a gene encoding a polypeptide having a Zn(2)Cys(6) domain or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17. In yet further examples, a construct for attenuating expression a gene encoding a Zn(2)Cys(6) domain-containing polypeptide can be a guide RNA or antisense oligonucleotide, where the sequence having homology to a transcribed region of a gene encoding a polypeptide having a Zn(2)Cys(6) domain in antisense orientation.

Further provided are guide RNAs for attenuating expression of a Zn(2)Cys(6) gene or a gene encoding a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, and DNA constructs encoding such guide RNAs. The guide RNAs can be chimeric or single guide RNAs or can be guide RNAs that include a tracr mate sequence but require an additional tracr RNA to effect genome editing. In various embodiments, provided herein is a nucleic acid molecule having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to at least a portion of SEQ ID NO: 1 or any of SEQ ID NOs:72-84, where the nucleic acid molecule encodes a guide RNA of a CRISPR system, that can be, as nonlimiting examples, a Cas9/CRISPR system or a Cpfl CRISPR system. The nucleic acid molecule can include, for example at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, or at least 25 nucleotides of sequence of a naturally occurring Zn(2)Cys(6) gene, such as SEQ ID NO: 1 or any of SEQ ID NOs:72-84. In exemplary embodiments, the guide RNA or nucleic acid sequence encoding the guide RNA can include any of SEQ ID NOs:51-62 or sequences having at least 88% or 93% identity to any thereof.

In addition, provided herein are antisense, ribozyme, or RNAi constructs that include at least a portion of a gene having encoding a Zn(2)Cys(6) or a polypeptide having at least 60% identity to any of SEQ ID NO:2 and SEQ ID NOs:5-17, in which a promoter, such as a heterologous promoter, is operably linked to the Zn(2)Cys(6) gene sequence and the Zn(2)Cys(6) gene sequence is in antisense orientation.

Further, provided herein are constructs for homologous recombination that include at least one sequence from a Zn(2)Cys(6) gene locus of the genome of an alga juxtaposed with a heterologous nucleic acid sequence that can be, in nonlimiting examples, a selectable marker or detectable marker gene. In some examples a construct for homologous recombination includes two nucleic acid sequences from a Zn(2)Cys(6) gene locus of the genome of an alga where the two sequences flank a heterologous sequence for insertion into the Zn(2)Cys(6) gene locus.

One skilled in the art will appreciate that a number of transformation methods can be used for genetic transformation of microorganisms and, therefore, can be deployed for the methods of the present invention. “Stable transformation” is intended to mean that the nucleic acid construct introduced into an organism integrates into the genome of the organism or is part of a stable episomal construct and is capable of being inherited by the progeny thereof. “Transient transformation” is intended to mean that a polynucleotide is introduced into the organism and does not integrate into the genome or otherwise become established and stably inherited by successive generations.

Genetic transformation can result in stable insertion and/or expression of transgenes, constructs from either the nucleus or the plastid, and in some cases can result in transient expression of transgenes. The transformation methods can also be used for the introduction of guide RNAs or editing DNAs. Genetic transformation of microalgae has been reported successful for more than 30 different strains of microalgae, which belong to at least ˜22 species of green, red, and brown algae, diatoms, euglenids, and dianoflagellates (see, e.g., Radakovits et al., Eukaryotic Cell, 2010; and Gong et al., J. Ind. Microbiol. Biotechnol., 2011). Non-limiting examples of such useful transformation methods include agitation of cells in the presence of glass beads or silicon carbide whiskers as reported by, for example, Dunahay, Biotechniques, 15(3):452-460, 1993; Kindle, Proc. Natl. Acad. Sci. U.S.A., 1990; Michael and Miller, Plant J., 13, 427-435, 1998. Electroporation techniques have been successfully used for genetic transformation of several microalgal species including Nannochloropsis sp. (see, e.g., Chen et al., J Phycol., 44:768-76, 2008), Chlorella sp. (see, e.g., Chen et al., Curr. Genet., 39:365-370, 2001; Chow and Tung, Plant Cell Rep. Vol. 18, No. 9, 778-780, 1999), Chlamydomonas (Shimogawara et al., Genetics, 148: 1821-1828, 1998), Dunaliella (Sun et al., Mol. Biotechnol., 30(3): 185-192, 2005). Micro-projectile bombardment, also referred to as microparticle bombardment, gene gun transformation, or biolistic bombardment, has been used successfully for several algal species including, for example, diatoms species such as Phaeodactylum (Apt et al., Mol. Gen. Genet., 252:572-579, 1996), Cyclotella and Navicula (Dunahay et al., J. Phycol., 31:1004-1012, 1995), Cylindrotheca (Fischer et al., J Phycol., 35:113-120, 1999), and Chaetoceros sp. (Miyagawa-Yamaguchi et al., Phycol. Res. 59: 113-119, 2011), as well as green algal species such as Chlorella (El-Sheekh, Biologia Plantarum, Vol. 42, No. 2: 209-216, 1999), and Volvox species (Jakobiak et al., Protist, 155:381-93, 2004). Additionally, Agrobacterium-mediated gene transfer techniques can also be useful for genetic transformation of microalgae, as has been reported by, for example, Kumar, Plant Sci., 166(3):731-738, 2004, and Cheney et al., J Phycol., Vol. 37, Suppl. 11, 2001.

A transformation vector or construct as described herein will typically comprise a marker gene that confers a selectable or scorable phenotype on target host cells, e.g., algal cells or may be co-transformed with a construct that includes a marker. A number of selectable markers have been successfully developed for efficient isolation of genetic transformants of algae. Common selectable markers include antibiotic resistance, fluorescent markers, and biochemical markers. Several different antibiotic resistance genes have been used successfully for selection of microalgal transformants, including blastocydin, bleomycin (see, for example, Apt et al., 1996, supra; Fischer et al., 1999, supra; Fuhrmann et al., Plant J., 19, 353-61, 1999, Lumbreras et al., Plant J., 14(4):441-447, 1998; Zaslavskaia et al., J. Phycol., 36:379-386, 2000), spectinomycin (Cerutti et al., Genetics, 145: 97-110, 1997; Doetsch et al., Curr. Genet., 39, 49-60, 2001; Fargo, Mol. Cell. Biol., 19:6980-90, 1999), streptomycin (Berthold et al., Protist, 153:401-412, 2002), paromomycin (Jakobiak et al., Protist, supra.; Sizova et al., Gene, 277:221-229, 2001), nourseothricin (Zaslavskaia et al., 2000, supra), G418 (Dunahay et al., 1995, supra; Poulsen and Kroger, FEBS Lett., 272:3413-3423, 2005, Zaslavskaia et al., 2000, supra), hygromycin (Berthold et al., 2002, supra), chloramphenicol (Poulsen and Kroger, 2005, supra), and many others. Additional selectable markers for use in microalgae such as Chlamydomonas can be markers that provide resistance to kanamycin and amikacin resistance (Bateman, Mol. Gen. Genet. 263:404-10, 2000), zeomycin and phleomycin (e.g., ZEOCIN™ pheomycin D1) resistance (Stevens, Mol. Gen. Genet. 251:23-30, 1996), and paramomycin and neomycin resistance (Sizova et al., 2001, supra). Other fluorescent or chromogenic markers that have been used include luciferase (Falciatore et al., J. Mar. Biotechnol., 1: 239-251, 1999; Fuhrmann et al., Plant Mol. Biol., 2004; Jarvis and Brown, Curr. Genet., 19: 317-322, 1991), 0-glucuronidase (Chen et al., 2001, supra; Cheney et al., 2001, supra; Chow and Tung, 1999, supra; El-Sheekh, 1999, supra; Falciatore et al., 1999, supra; Kubler et al., J Mar. Biotechnol., 1:165-169, 1994), β-galactosidase (Gan et al., J Appl. Phycol., 15:345-349, 2003; Jiang et al., Plant Cell Rep., 21:1211-1216, 2003; Qin et al., High Technol. Lett., 13:87-89, 2003), and green fluorescent protein (GFP) (Cheney et al., 2001, supra; Ender et al., Plant Cell, 2002, Franklin et al., Plant J., 2002; 56, 148, 210).

One skilled in the art will readily appreciate that a variety of known promoter sequences can be usefully deployed for transformation systems of microalgal species in accordance with the present invention. For example, the promoters commonly used to drive transgene expression in microalgae include various versions of the of cauliflower mosaic virus promoter 35S (CaMV35S), which has been used in both dinoflagellates and chlorophyta (Chow et al, Plant Cell Rep., 18:778-780, 1999; Jarvis and Brown, Curr. Genet., 317-321, 1991; Lohuis and Miller, PlantJ., 13:427-435, 1998). The SV40 promoter from simian virus has also reported to be active in several algae (Gan et al., J. Appl. Phycol., 151 345-349, 2003; Qin et al., Hydrobiologia 398-399, 469-472, 1999). The promoters of RBCS2 (ribulose bisphosphate carboxylase, small subunit) (Fuhrmann et al., Plant J., 19:353-361, 1999) and PsaD (abundant protein of photosystem I complex; Fischer and Rochaix, FEBS Lett. 581:5555-5560, 2001) from Chlamydomonas can also be useful. The fusion promoters of HSP70A/RBCS2 and HSP70A/02TUB (tubulin) (Schroda et al., Plant J., 21:121-131, 2000) can also be useful for an improved expression of transgenes, in which HSP70A promoter may serve as a transcriptional activator when placed upstream of other promoters. High-level expression of a gene of interest can also be achieved in, for example diatoms species, under the control of a promoter of anfcp gene encoding a diatom fucoxanthin-chlorophyll a/b binding protein (Falciatore et al., Mar. Biotechnol., 1:239-251, 1999; Zaslavskaia et al., J. Phycol. 36:379-386, 2000) or the vcp gene encoding a eustigmatophyte violaxanthin-chlorophyll a/b binding protein (see U.S. Pat. No. 8,318,482). If so desired, inducible promoters can provide rapid and tightly controlled expression of genes in transgenic microalgae. For example, promoter regions of the NR genes encoding nitrate reductase can be used as such inducible promoters. The NR promoter activity is typically suppressed by ammonium and induced when ammonium is replaced by nitrate (Poulsen and Kroger, FEBS Lett 272:3413-3423, 2005), thus gene expression can be switched off or on when microalgal cells are grown in the presence of ammonium/nitrate. Additional algal promoters that can find use in the constructs and transformation systems provided herein include those disclosed in U.S. Pat. No. 8,883,993; U.S. Patent Appl. Pub. No. US 2013/0023035; U.S. Patent Application Pub. No. US 2013/0323780; and U.S. Patent Application Pub. No. US 2014/0363892.

Host cells can be either untransformed cells or cells that are already transfected with at least one nucleic acid molecule. For example, an algal host cell that is engineered to have attenuated expression of a lipid regulator gene can further include one or more genes that may confer any desirable trait, such as, but not limited to, increased production of biomolecules of interest, such as one or more proteins, pigments, alcohols, or lipids.

Methods of Producing Lipids

Also provided herein are methods of producing lipid by culturing a mutant microorganism as provided herein that has increased lipid productivity with respect to a control cell while producing at least 45% of the biomass produced by a control cell under the same culture conditions. The methods include culturing a mutant microorganism as provided herein in a suitable medium to produce lipid and recovering biomass or at least one lipid from the culture. The microorganism can in some examples be an alga, and the culture can be a photoautotrophic culture. Culturing can be in batch, semi-continuous, or continuous mode.

The mutant microorganism in some examples can be cultured in a medium that comprises less than about 5 mM ammonium, for example, less than about 2.5 mM ammonium, less than about 2 mM ammonium, less than about 1.5 mM ammonium, less than or equal to about 1 mM ammonium, or less than or equal to about 0.5 mM. The culture medium can include, for example, from about 0 to about 2.5 mM ammonium, from about 0.1 to about 2.5 mM ammonium, from about 0.5 to about 2.5 mM ammonium, from about 0 to about 1.5 mM ammonium, from about 0.1 to about 1 mM ammonium, or from about 0.2 to about 1 mM ammonium. The microorganism can be cultured in a medium that includes nitrate, which in some examples may be substantially the sole nitrogen source in the culture medium or may be present in addition to less than 5 mM ammonium, less than 2.5 mM ammonium, less than 1.0 mM ammonium, or less than or equal to about 0.5 mM ammonium. Alternatively or in addition, the culture medium can comprises urea, which in some examples can be substantially the sole source of nitrogen in the culture medium.

Yet another aspect of the invention is a method of producing lipid that includes culturing a microorganism under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, and isolating lipid from the microorganism, the culture medium, or both. For example, the microorganisms can be cultured such that the FAME to TOC ratio is maintained at between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. The ratio can be maintained at between about 0.3 and about 0.8, for example between about 0.4 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55 for at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 15, at least 20, at least 30 days, or at least 60 days. In these methods the microorganism can be cultured under continuous or semi-continuous conditions. The method of producing lipid can include culturing a mutant microorganism such as any provided herein under conditions in which the FAME to TOC ratio of the microorganism is maintained between about 0.3 and about 0.8, between about 0.3 and about 0.8, between about 0.4 and about 0.7, between about 0.4 and about 0.6, or between about 0.45 and about 0.55. For example, the microorganism can be a mutant microorganism having attenuated expression of a gene encoding a polypeptide having at least 55%, at least 65%, at least 75%, or at least 85% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17. The FAME to TOC ratio may be adjusted, for example, by the type and concentration of nitrogen source present in the culture medium. For example, the method may include culturing a microorganism, such as a mutant microorganism as disclosed herein, in a culture medium that includes nitrate and less than 2.5 mM ammonium or less than 1.0 mM ammonium.

The culture conditions in the methods provided herein are preferably conditions in which a control microorganism (i.e., a microorganism that does not have the mutation leading to higher lipid productivity) produces biomass on a daily basis, for example, produces biomass on a daily basis for at least five, at least eight, at least ten, or at least twelve days, and in various embodiments the methods of producing lipid result in the mutant microorganism producing at least 50% more lipid than a control microorganism while exhibiting a decrease in biomass (e.g., TOC) accumulation of no more than 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, or 1% with respect to the control microorganism. For example, the methods of producing lipid can include culturing a mutant microorganism as provided herein in a suitable medium to produce lipid and recovering biomass or at least one lipid from the culture, in which the mutant microorganism produces at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 110%, at least 120% more lipid than a control microorganism while producing at least 65%, 70%, 75%, 880%, 85%, 90%, 95%, 98%, or 99% of the biomass produced by the control microorganism, under conditions where both the mutant microorganism and the control microorganism are producing biomass on a daily basis. The microorganism can in some examples be an alga, and the culture can be a photoautotrophic culture. Culturing can be in batch, semi-continuous, or continuous mode.

The lipid producing microorganisms may be cultured in any suitable vessel(s), including flasks or bioreactors, where the algae may be exposed to artificial or natural light (or natural light supplemented with artificial light). The culture comprising mutant algae that are deregulated in their response to low light may be cultured on a light/dark cycle that may be, for example, a natural or programmed light/dark cycle, and as illustrative examples, may provide twelve hours of light to twelve hours of darkness, fourteen hours of light to ten hours of darkness, sixteen hours of light to eight hours of darkness, etc.

Culturing refers to the intentional fostering of growth (e.g., increases in cell size, cellular contents, and/or cellular activity) and/or propagation (e.g., increases in cell numbers via mitosis) of one or more cells by use of selected and/or controlled conditions. The combination of both growth and propagation may be termed proliferation. A microorganism as provided herein may be cultured for at least five, at least six, at least seven at least eight, at least nine, at least ten, at least eleven at least twelve, at least thirteen, at least fourteen, or at least fifteen days, or at least one, two three, four, five, six, seven, eight, nine, or ten weeks, or longer.

Non-limiting examples of selected and/or controlled conditions that can be used for culturing the recombinant microorganism can include the use of a defined medium (with known characteristics such as pH, ionic strength, and/or carbon source), specified temperature, oxygen tension, carbon dioxide levels, growth in a bioreactor, or the like, or combinations thereof. In some embodiments, the microorganism or host cell can be grown mixotrophically, using both light and a reduced carbon source. Alternatively, the microorganism or host cell can be cultured phototrophically. When growing phototrophically, the algal strain can advantageously use light as an energy source. An inorganic carbon source, such as CO₂ or bicarbonate can be used for synthesis of biomolecules by the microorganism. “Inorganic carbon”, as used herein, includes carbon-containing compounds or molecules that cannot be used as a sustainable energy source by an organism. Typically “inorganic carbon” can be in the form of CO₂ (carbon dioxide), carbonic acid, bicarbonate salts, carbonate salts, hydrogen carbonate salts, or the like, or combinations thereof, which cannot be further oxidized for sustainable energy nor used as a source of reducing power by organisms. A microorganism grown photoautotrophically can be grown on a culture medium in which inorganic carbon is substantially the sole source of carbon. For example, in a culture in which inorganic carbon is substantially the sole source of carbon, any organic (reduced) carbon molecule or organic carbon compound that may be provided in the culture medium either cannot be taken up and/or metabolized by the cell for energy and/or is not present in an amount sufficient to provide sustainable energy for the growth and proliferation of the cell culture.

Microorganisms and host cells that can be useful in accordance with the methods of the present invention can be found in various locations and environments throughout the world. The particular growth medium for optimal propagation and generation of lipid and/or other products can vary and may be optimized to promote growth, propagation, or production of a product such as a lipid, protein, pigment, antioxidant, etc. In some cases, certain strains of microorganisms may be unable to grow in a particular growth medium because of the presence of some inhibitory component or the absence of some essential nutritional requirement of the particular strain of microorganism or host cell.

Solid and liquid growth media are generally available from a wide variety of sources, as are instructions for the preparation of particular media suitable for a wide variety of strains of microorganisms. For example, various fresh water and salt water media can include those described in Barsanti (2005) Algae: Anatomy, Biochemistry & Biotechnology, CRC Press for media and methods for culturing algae. Algal media recipes can also be found at the websites of various algal culture collections, including, as nonlimiting examples, the UTEX Culture Collection of Algae (www.sbs.utexas.edu/utex/media.aspx); Culture Collection of Algae and Protozoa (www.ccap.ac.uk); and Katedra Botaniky (botany.natur.cuni.cz/algo/caup-media.html).

The culture methods can optionally include inducing expression of one or more genes and/or regulating a metabolic pathway in the microorganism. Inducing expression can include adding a nutrient or compound to the culture, removing one or more components from the culture medium, increasing or decreasing light and/or temperature, and/or other manipulations that promote expression of the gene of interest. Such manipulations can largely depend on the nature of the (heterologous) promoter operably linked to the gene of interest.

In some embodiments of the present invention, the microorganisms having increased lipid productivity can be cultured in a “photobioreactor” equipped with an artificial light source, and/or having one or more walls that is transparent enough to light, including sunlight, to enable, facilitate, and/or maintain acceptable microorganism growth and proliferation. For production of fatty acid products or triglycerides, photosynthetic microorganisms or host cells can additionally or alternately be cultured in shake flasks, test tubes, vials, microtiter dishes, petri dishes, or the like, or combinations thereof.

Additionally or alternately, mutant or recombinant photosynthetic microorganisms or host cells may be grown in ponds, canals, sea-based growth containers, trenches, raceways, channels, or the like, or combinations thereof. In such systems, the temperature may be unregulated, or various heating or cooling method or devices may be employed As with standard bioreactors, a source of inorganic carbon (such as, but not limited to, CO₂, bicarbonate, carbonate salts, and the like), including, but not limited to, air, CO₂-enriched air, flue gas, or the like, or combinations thereof, can be supplied to the culture. When supplying flue gas and/or other sources of inorganic that may contain CO in addition to CO₂, it may be necessary to pre-treat such sources such that the CO level introduced into the (photo)bioreactor do not constitute a dangerous and/or lethal dose with respect to the growth, proliferation, and/or survival of the microorganisms.

The mutant microorganisms can include one or more non-native genes encoding a polypeptide for the production of a product, such as but not limited to a lipid.

The methods include culturing a mutant microorganism as provided herein, such as a mutant microorganism as provided herein that has increased lipid productivity with respect to a control cell while producing at least 50% of the biomass produced by a control cell under the same culture conditions to produce biomass or lipid. Lipids can be recovered from culture by recovery means known to those of ordinary skill in the art, such as by whole culture extraction, for example, using organic solvents or by first isolating biomass from which lipids are extracted (see, for example, Hussein et al. Appl. Biochem. Biotechnol. 175:3048-3057; Grima et al. (2003) Biotechnol. Advances 20:491-515). In some cases, recovery of fatty acid products can be enhanced by homogenization of the cells (Gunerken et al. (2015) Biotechnol. Advances 33:243-260). For example, lipids such as fatty acids, fatty acid derivatives, and/or triglycerides can be isolated from algae by extraction of the algae with a solvent at elevated temperature and/or pressure, as described in the co-pending, commonly-assigned U.S. patent application Ser. No. 13/407,817 entitled “Solvent Extraction of Products from Algae”, filed on Feb. 29, 2012, which is incorporated herein by reference in its entirety.

Biomass can be harvested, for example, by centrifugation or filtering. The biomass may be dried and/or frozen. Further products may be isolated from biomass, such as, for example, various lipids or one or more proteins. Also included in the invention is an algal biomass comprising biomass of lipid regulator mutant, such as any disclosed herein, such as but not limited to a lipid regulator mutant that includes a mutation in a gene encoding a polypeptide having at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2 and SEQ ID NOs:5-17.

ADDITIONAL EMBODIMENTS

Alternatively or in addition to any of the forgoing embodiments, the invention provides the following embodiments:

Embodiment 1 is a mutant microorganism that produces at least 25% more lipid and at least 45% more biomass than is produced by a control microorganism cultured under substantially identical conditions in which the control microorganism produces biomass, optionally wherein any one or more of the following are fulfilled:

-   -   (a) the control microorganism is a wild type microorganism;     -   (b) the mutant microorganism produces at least 45%, at least         50%, at least 55%, at least 60%, at least 65%, at least 70%, at         least 75%, at least 80%, at least 85%, at least 90%, at least         95%, at least 100%, as much biomass, which can be assessed as         average biomass (e.g., TOC) productivity per day, during a         culture period of at least three, at least four, at least five,         at least six, at least seven, at least eight, at least nine, at         least ten, at least eleven, at least twelve, at least thirteen         days, at least fourteen, at least fifteen, at least twenty, at         least thirty, or at least sixty days;     -   (c) the mutant microorganism produces at least 25%, at least         30%, at least 55%, at least 40%, at least 45%, at least 50%, at         least 55%, at least 60%, at least 70%, at least 75%, at least         80%, at least 85%, at least 90%, at least 95%, at least 100%, at         least 110%, at least 115%, at least 120%, at least 150% more         lipid, or at least 200% more lipid, which can be assessed as         average lipid (e.g., FAME) productivity per day, than is         produced by a control microorganism during a culture period of         at least at least three, at least four, at least five, at least         six, at least seven, at least eight, at least nine, at least         ten, at least eleven, at least twelve, at least thirteen days,         at least fourteen, at least fifteen, at least twenty, at least         thirty, or at least sixty days;     -   (d) the substantially identical conditions in which the control         microorganism produces biomass comprise a culture medium that         comprises less than about 5 mM, less than about 4 mM, less than         about 3 mM, less than 2.5 mM ammonium, less than 2 mM ammonium,         less than 1.5 mM ammonium, less than or equal to about 1 mM         ammonium, or less than or equal to about 0.5 mM ammonium;     -   (e) the substantially identical conditions in which the control         microorganism produces biomass comprise a culture medium that         comprises nitrate or urea; and/or     -   (f) the microorganism is a heterokont or alga.

Embodiment 2 is a mutant microorganism according to embodiment 1 in which the mutant has attenuated expression of a regulator gene wherein the regulator gene encodes a polypeptide having at least 50, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, or SEQ ID NO: 18 and/or regulator gene encodes a polypeptide that includes a Zn(2)Cys(6) domain, optionally wherein the polypeptide further includes a PAS3 domain.

Embodiment 3 is a mutant microorganism according to embodiment 1 or embodiment 2, wherein the mutant is a spontaneous mutant, a classically-derived mutant, or an engineered mutant, optionally wherein the mutant is an engineered mutants that:

-   -   (a) has a disrupted gene, optionally wherein the gene is         disrupted in a noncoding region;     -   (b) is deleted in all or a portion of a gene;     -   (c) includes an antisense construct, an RNAi construct, or a         ribozyme construct that targets a gene;     -   (d) includes an insertion, optionally wherein the insertion is         generated by CRISPR/cas genome editing; and/or     -   (e) includes a mutation generated by CRISPR/cas genome editing.

Embodiment 4 is a mutant microorganism according to any of embodiments 1-3, wherein:

-   -   (a) the mutant produces at least 50% or at least 80% or at least         100% more FAME (e.g., average productivity per day) while         producing at least 85% or at least 90% or at least 95% of the         TOC produced by a control cell, e.g., TOC productivity on a per         day basis, when cultured under conditions in which both the         control and mutant microorganism produce biomass; and/or     -   (b) wherein the FAME/TOC ratio of the mutant microorganism is at         least 40%, at least 50%, at least 60%, at least 70%, or at least         75% higher than the FAME/TOC of the control microorganism while         producing at least 85% or at least 90% of the TOC produced by a         control cell (such as a wild type cell) when cultured under         conditions in which both the control and mutant microorganism         produce biomass; and/or     -   (c) the FAME/TOC ratio of the mutant microorganism is at least         0.30, at least 0.35 at least 0.40, at least 0.5, or between         about 0.3 and about 0.8 when cultured under conditions in which         both the control and mutant microorganism produce biomass and/or     -   (d) wherein the FAME/TOC ratio is maintained between about 0.3         and about 0.7 for a culture period of at least five, at least         six, at least seven, at least eight, at least nine, at least         ten, at least eleven, at least twelve, or at least thirteen days         during which the mutant microorganism produces at least 50%, at         least 60%, at least 70%, or at least 75%, at least 80% or at         least 85% of the biomass produced by a control microorganism         cultured under the same conditions in which the control         microorganism accumulates biomass.

Embodiment 6 is a mutant microorganism according to any of embodiments 1-3, wherein:

-   -   (a) the mutant produces at least 85%, at least 90%, at least         95%, at least 100%, at least 105%, at least 110%, or at least         115% more FAME (e.g., on an average per day basis) while         producing at least 70%, at least 75%, at least 80%, or at least         85% of the TOC produced (e.g., on an average per day basis) by a         control microorganism (such as a wild type cell) when cultured         under conditions in which both wild type and mutant         microorganism are producing biomass; and/or     -   (b) the FAME/TOC ratio of the mutant microorganism is at least         100%, at least 110%, at least 120%, at least 130%, at least         140%, at least 150%, at least 160%, at least 170%, or at least         180% greater than the FAME/TOC ratio of a control microorganism         when cultured under conditions in which both wild type and         mutant microorganism are producing biomass; and/or     -   (c) the FAME/TOC ratio of the mutant microorganism is at least         0.50, at least 0.55, at least 0.60, at least 0.65, at least         0.70, or at least 0.75 and the mutant microorganism produces at         least 70%, at least 75%, at least 80%, or at least 85% of the         TOC produced by a control microorganism when cultured under         conditions in which the wild type accumulates biomass.

Embodiment 7 is a mutant microorganism according to any of embodiments 1-6, wherein:

-   -   (a) the culture conditions under which the mutant microorganism         produces more lipid is batch, semi-continuous, or continuous         culture; and/or     -   (b) the daily lipid productivity of the mutant is greater than         the daily lipid productivity of the control microorganism         throughout the culture period.

Embodiment 8 is a mutant microorganism according to any of embodiments 1-7 in which the mutant microorganism comprises a mutation in a non-coding region of a gene that reduces expression of the gene, optionally wherein the mutation is an insertion.

Embodiment 9 is a mutant microorganism according to any of embodiments 1-7 in which the mutant microorganism comprises a construct that reduces expression of a gene, wherein the construct encodes an RNAi, antisense transcript, or ribozyme.

Embodiment 10 is a mutant microorganism according to any of embodiments 1-9, wherein the mutant microorganism is a Labyrinthulomycte species,

-   -   (a) optionally wherein the mutant microorganism is a species         belonging to any of the genera Labryinthula, Labryinthuloides,         Thraustochytrium, Schizochytrium, Aplanochytrium,         Aurantiochytrium, Oblongichytrium, Japonochytrium, Diplophrys,         or Ulkenia; or wherein the mutant microorganism is an algal         species,     -   (b) optionally a species belonging to any of the genera         Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas,         Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus,         Bracteococcus, Chaetoceros, Carteria, Chlamydomonas,         Chlorococcum, Chlorogonium, Chlorella, Chroomonas,         Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas,         Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania,         Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia,         Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus,         Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis,         Micractinium, Monodus, Monoraphidium, Nannochloris,         Nannochloropsis, Navicula, Neochloris, Nephrochloris,         Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis,         Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova,         Pelagomonas, Phceodactylum, Phagus, Picochlorum, Platymonas,         Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella,         Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys,         Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra,         Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira,         Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox.

Embodiment 11 is biomass comprising any of the mutant microorganisms of any of embodiments 1-10.

Embodiment 12 is a nucleic acid molecule comprising a sequence encoding a polypeptide having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO:17;

-   -   wherein any one or more of the following are satisfied:         -   (a) the polypeptide includes an amino acid sequence encoding             a Zn(2)Cys(6) domain, optionally wherein the Zn(2)Cys(6)             domain has at least 60%, at least 65%, at least 70%, or at             least 75%, at least 80%, at least 85%, at least 90%, or at             least 95% identity to SEQ ID NO:3;     -   the polypeptide includes an amino acid sequence encoding a PAS         domain, optionally wherein the PAS domain has at least 60%, at         least 65%, at least 70%, or at least 75%, at least 80%, at least         85%, at least 90%, or at least 95% identity to any of SEQ ID         NO:21-SEQ ID NO:25;         -   (b) the nucleic acid molecule in various examples comprises             a cDNA that lacks one or more introns present in the             naturally-occurring gene or is a gene construct that             includes one or more introns not present in the             naturally-occurring gene;         -   (c) the nucleic acid molecule in various examples can have a             sequence that is not 100% identical to a naturally-occurring             gene;         -   (d) the nucleic acid molecule has at least 50%, at least             55%, at least 60%, at least 65%, at least 70%, or at least             75%, at least 80%, at least 85%, at least 90%, or at least             95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ             ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO:             11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15,             SEQ ID NO:16, or SEQ ID NO: 17;         -   (e) the nucleic acid molecule comprises a heterologous             promoter operably linked to the sequence; and/or         -   (f) the nucleic acid molecule comprises a vector.

Embodiment 13 is a nucleic acid molecule construct for attenuating expression of a gene encoding a polypeptide according to having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, or SEQ ID NO: 17;

-   -   a sequence encoding a guide RNA of a CRISPR system, an RNAi         construct, an antisense construct, a ribozyme construct, or a         construct for homologous recombination, e.g., a construct having         one or more nucleotide sequences having homology to a         naturally-occurring Zn(2)Cys(6) domain-encoding gene as         disclosed herein and/or sequences adjacent thereto in the native         genome from which the gene is derived.

Embodiment 14 is method of engineering a cell for increased lipid production comprising attenuating expression of a gene encoding a polypeptide having at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, or SEQ ID NO: 17, optionally a gene encoding a polypeptide having an amino acid sequence having at least 55%, at least 60%, at least 65%, at least 70%, or at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% identity to any of SEQ ID NOs:21-25, into a microorganism to produce a mutant microorganism having higher lipid productivity than the progenitor microorganism, optionally wherein attenuating expression of the gene comprises introducing a nucleic acid molecule according to embodiment 13 into the microorganism.

Embodiment 15 is method for producing lipid comprising culturing a mutant according to any of embodiments 1-10 to produce lipid, optionally wherein any one or more of the following are satisfied:

-   -   (a) the culture medium includes nitrate or urea;     -   (b) the culture medium includes less than 5 mM, less than 4 mM,         less than 3 mM, less than 2.5 mM ammonium, less than 2 mM         ammonium, less than or equal to about 1.5 mM ammonium, less than         or equal to about 1 mM ammonium, or less than or equal to about         0.5 mM ammonium;     -   (c) the culture is a batch, semi-continuous, or continuous         culture;     -   (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13         day, at least 15, 20, 30, 40, 50, or 60 days;     -   (e) the mutant is an algal mutant and the culture is         photoautotrophic;     -   (f) the mutant produces at least 25% more lipid, such as at         least 50% more lipid, preferably FAME lipid, and at least 65% of         the biomass of a control microorganism during the culture         period;     -   (g) the mutant produces more lipid, preferably FAME lipid, on         each day of the culture period; and/or     -   (h) the mutant accumulates biomass on each day of the culture         period.

Embodiment 16 is method for producing lipid comprising culturing a microorganism under conditions in which the FAME/TOC ratio is maintained at between about 0.3 and about 0.8 throughout the culture period, optionally wherein any one or more of the following are satisfied:

-   -   (a) the culture medium includes nitrate or urea;     -   (b) the culture medium includes less than 5 mM, less than 4 mM,         less than 3 mM, less than 2.5 mM ammonium, less than 2 mM         ammonium, less than or equal to about 1.5 mM ammonium, less than         or equal to about 1 mM ammonium, or less than or equal to about         0.5 mM ammonium;     -   (c) the culture is a batch, semi-continuous, or continuous         culture;     -   (d) the culture period is at least 5, 7, 8, 9, 10, 11, 12, 13         day, at least 15, 20, 30, 40, 50, or 60 days;     -   (e) the microorganism is an algal microorganism and the culture         is photoautotrophic;     -   (f) the microorganism accumulates biomass on each day of the         culture period; and/or     -   (g) the microorganism is a mutant microorganism according to any         of embodiments 1-1

EXAMPLES Media Used in Examples

The following media are used in the Examples.

PM066 medium (Example 1) includes 8.8 mM nitrate as the sole nitrogen source. PM066 medium included 10 mM nitrate (NO₃) and 0.417 mM phosphate (PO₄) along with trace metals and vitamins in Instant Ocean salts. PM066 media was made by adding 5.71 ml of a 1.75 M NaNO₃ stock solution (148.7 g/L), and 5.41 ml of a 77 mM K₂HPO₄.3H₂O stock solution (17.57 g/L) to 981 mls of Instant Ocean salts solution (35 g/L) along with 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution. Chelated Metals Stock Solution was prepared by adding to 400 mls of water 2.18 g Na₂EDTA-2H₂O; 1.575 g FeCl₃.6H₂O; 500 μl of 39.2 mM stock solution (0.98 g/100 ml) CuSO₄.5H₂O; 500 μl of 77.5 mM stock solution (2.23 g/100 ml) ZnSO₄.7H₂O; 500 μl of 42.0 mM stock solution (1.00 g/100 ml) CoCl₂.6H₂O; 500 μl of 910.0 mM stock solution (18.0/100 ml) MnCl₂.4H₂O; 500 μl of 26.0 mM stock solution (0.63 g/100 ml) Na₂MoO₄.2H₂O; bringing up to 500 ml final volume, and filter sterilizing. Vitamin Stock Solution was prepared by adding to 400 mls of water 0.05 g Thiamine HCl; 500 μl of 0.37 mM stock solution (0.05 g/100 ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stock solution (0.01 g/100 ml) of biotin, bringing up to a final volume of 500 mls, and filter sterilizing.

PM067 medium included no nitrogen source (no nitrate, ammonium, or urea), and 0.417 mM phosphate (PO₄) along with trace metals and vitamins in Instant Ocean salts. PM067 media was made by adding 5.41 ml of a 77 mM K₂HPO₄ 3H₂O stock solution (17.57 g/L) to 987 mls of Instant Ocean salts solution (35 g/L) along with 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution. Chelated Metals Stock Solution was prepared by adding to 400 mls of water 2.18 g Na₂EDTA-2H₂O; 1.575 g FeCl₃.6H₂O; 500 μl of 39.2 mM stock solution (0.98 g/100 ml) CuSO₄.5H₂O; 500 μl of 77.5 mM stock solution (2.23 g/100 ml) ZnSO₄.7H₂O; 500 μl of 42.0 mM stock solution (1.00 g/100 ml) CoCl₂.6H₂O; 500 μl of 910.0 mM stock solution (18.0/100 ml) MnCl₂.4H₂O; 500 μl of 26.0 mM stock solution (0.63 g/100 ml) Na₂MoO₄.2H₂O; bringing up to 500 ml final volume, and filter sterilizing. Vitamin Stock Solution was prepared by adding to 400 mls of water 0.05 g Thiamine HCl; 500 μl of 0.37 mM stock solution (0.05 g/100 ml) of cyanocobalamin; and 2.5 ml of 0.41 mM stock solution (0.01 g/100 ml) of biotin, bringing up to a final volume of 500 mls, and filter sterilizing.

PM074 is a nitrogen replete (“nitrate-only”) medium (includes nitrate as substantially the sole nitrogen source) that is 10× F/2 made by adding 1.3 ml PROLINE® F/2 Algae Feed Part A (Aquatic Eco-Systems) and 1.3 ml PROLINE® F/2 Algae Feed Part B (Aquatic Eco-Systems) to a final volume of 1 liter of a solution of Instant Ocean salts (35 g/L) (Aquatic Eco Systems, Apopka, Fla.). Proline A and Proline B together include 8.8 mM NaNO₃, 0.361 mM NaH₂PO₄.H₂O, 10× F/2 Trace metals, and 10× F/2 Vitamins (Vuillard (1975) Culture of phytoplankton for feeding marine invertebrates in “Culture of Marine Invertebrate Animals.” (eds: Smith W. L. and Chanley M. H.) Plenum Press, New York, USA. pp 26-60).

PM123 medium is PM074 medium supplemented with additional Proline B so that the concentration of nitrate was increased from approximately 8.8 mM to approximately 15 mM. This is also a “nitrate only” medium.

PM124 medium is PM074 supplemented with 5 mM ammonium and 10 mM HEPES pH 8.0. It is made by adding 10 mls of 1 M HEPES pH 8 and 5 mls of NH₄Cl to the PM074 recipe (final volume of 1 L). In some examples, additional media with controlled ammonium levels was made by adjusting the ammonium concentration of PM074 and adding additional Hepes buffer.

PM125 medium (Example 5): includes 7.5 mM urea as the only source of nitrogen available to the cells. To 1× instant ocean was added (while mixing): 3.75 ml 2M Urea stock solution, 0.32 ml 1 M NaH₂PO₄ stock solution, 4 ml of Chelated Metals Stock Solution and ml of 4 ml Vitamin Stock Solution (see above). The media was filter sterilized through ≤0.1 μm filter and stored at room temperature.

Example 1 Identification of a Zinc-Cys Domain Polypeptide Down-Regulated During Nitrogen Starvation

Various strains of Nannochloropsis accumulate high levels of triacylglycerols (TAG) storage lipid during nitrogen deprivation and correlations between increased TAG production and correlations between TAG accumulation and presumed underlying changes in gene expression in different metabolic pathways leading to TAG synthesis have been reported (Radakovits et al. (2012) Nat Commun 3: 686; Li et al. (2014) The Plant Cell 26: 1645-1665; Corteggiani Carpinelli et al. (2014) Mol Plant 7:1645-1665). To identify genes encoding regulators that influence lipid biosynthesis and accumulation, the early transcriptional response of Nannochloropsis cells subjected to N-deprivation (—N) was analyzed. A comparative transcriptomics experiment was performed in which the RNA transcript levels of genes of Nannochloropsis gaditana cells under nitrogen starvation, during which Nannochloropsis induces storage lipid biosynthesis, were compared with the levels of RNA transcripts of the same strain of Nannochloropsis gaditana grown under identical conditions except that the amount of nitrogen in the growth medium was not limiting.

Wild type N. gaditana (WT-3730) cells were grown in nutrient replete medium under a 16 hour light (120 μE)/8 hour dark cycle to light limitation (to O.D. of 1.25) and at the beginning of the photoperiod were spun down and resuspended in either nitrogen replete medium PM066 or culture medium lacking a nitrogen source (“nitrogen deplete” or “—N” medium PM067) and incubated under the provided light conditions. RNA was isolated from samples removed at various time intervals after resuspension of the cells in nitrogen replete (+N) or nitrogen deplete (−N) medium. Lipid accumulation was determined from samples taken throughout the assay. Lipid accumulation (measured as FAME as described in Example 4) was indistinguishable between nitrogen deplete and nitrogen replete cultures at the 3 h timepoint, but at 10 h FAME accumulation in the nitrogen deplete culture was double that of the nitrogen replete culture (FIG. 1A). Treatments were performed in biological triplicates. Under the assumption that transcriptional changes should precede metabolic changes, the 3 h time-point was selected for mRNA sequencing. Two samples for each treatment were sequenced.

RNA was isolated by spinning down 10 mLs of each algal cell culture (4000×g for 5 minutes) and decanting the supernatant. The pellets were resuspended in 1.8 mL Buffer A (5 mL TLE Grinding Buffer, 5 mL phenol, 1 mL 1-bromo-3-chloropropane and L mercaptoethanol, where TLE Grinding Buffer includes 9 mL of 1M Tris pH 8, 5 mL of 10% SDS, 0.6 mL of 7.5 M LiCl, and 450 μl 0.5 M EDTA in a final volume of 50 mL) and transferred to 2 mL microcentrifuge tubes containing approximately 0.5 mL of 200 μm zirconium beads. The tubes were vortexed vigorously for 5 min at 4° C. and then centrifuged for 2 min at 11.8×g. The aqueous layers were then removed and pipetted into new 2 mL tubes, to which 1 mL 25:24:1 phenol extraction buffer (25 mL phenol pH 8.1; 24 mL 1-bromo-3-chloropropane, and 1 mL isoamyl alcohol) was added. The tubes were shaken vigorously and centrifuged for 2 min at 11.8×g. After centrifugation, the aqueous layer was removed and pipetted into new 2 mL centrifuge tubes, to which 1 ml 1-bromo-3-chloropropane was added. The tubes were shaken and again centrifuged for 2 min at 11.8×g. The aqueous layer was removed to a new tube and 0.356 volumes of 7.5 M LiCl were added. The tubes were inverted 10-12 times and stored at −20° C. overnight. The next day, samples were allowed to come to room temperature without mixing and were centrifuged at 16,000×g for 30 minutes. The supernatants were removed and the pellets were washed with 1 mL of ice cold 80% ethanol. The tubes were centrifuged for 30 min at 16,000×g and allowed to air dry after the supernatants had been removed. Finally, the RNA pellets were resuspended in 50 μl ultrapure water. The RNA quality was assessed by on-chip gel electrophoresis using an Agilent 2100 Bioanalyzer and RNA6000 LabChip according to manufacturer instructions.

Next-generation sequencing libraries were prepared from the isolated RNA utilizing the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, Calif.) following manufacturer instructions. The TruSeq libraries were sequenced using sequencing-by-synthesis (Illumina MiSeq) to generate 100 bp paired-end reads using the mRNA-Seq procedure (described in Mortazavi et al. (2008) Nature Methods 5:621-628). Mappable reads were aligned to the N. gaditana reference genome sequence using TopHat (tophat.cbcb.umd.edu/). Expression levels were computed for every annotated gene using the Cuffdiff component of the Cufflinks software (cufflinks.cbcb.umd.edu). TopHat and Cufflinks are described in Trapnell et al. (2012) Nature Protocols 7: 562-578. Differential expression analysis was performed using the R package edgeR (McCarthy et al. (2012) Nucl. Acids Res. 40:doi:10/1093/nar/gks042)). Expression levels in units of fragments per kilobase per million (FPKM) were reported for every gene in each sample using standard parameters. FPKM is a measure of relative transcriptional levels that normalizes for differences in transcript length.

Global analysis of the transcriptome of −N and +N cultures at 3 h revealed 1064 differentially expressed genes having a difference in expression of greater than 1 fold and a false discovery rate (FDR) of less than 0.01. These genes are depicted as dots and Xs in the plot of FIG. 1B. Of these genes, 363 were upregulated (right side of the plot) and 701 were down-regulated in the −N condition (left side of the plot). The list of differentially expressed genes was compared with a bioinformatically curated list of putative Nannochloropsis transcription factors previously generated by mining the Nannochloropsis genome for proteins containing DNA binding domains and other conserved pfam domains typical of characterized transcription factors using the Plant Transcription Factor Database as a reference (Perez-Rodriguez et al. (2010) Nucl. Acids Res. 38: D822-D827; Jin et al. (2013) Nucl. Acids Res. 42: D1182-D1187). We found 20 transcription factors, represented as Xs in FIG. 1B and listed in Table 1, that were represented only in the down-regulated set of transcription factors. No transcription factors were found to be upregulated at the 3 h timepoint. N. gaditana gene identifiers are based on the genome sequence described in Corteggiani Carpinelli et al., Mol Plant 7, 323-335 (2014).

TABLE 1 Transcription Factors Targeted for Knockout by Cas9 PCR Positive Fold Lines/ Change Lines N. gaditana id Gene Description (log 2) FDR^(†) Screened Success^(††) Naga_100055g29 CCT domain protein −3.3 5.4E−15 13/31 Y Naga_100104g18 Zn(2)-C6 fungal-type DNA- −2.5 1.5E−19 19/29 Y binding domain protein Naga_100043g41 RpoD family RNA polymerase −1.6 5.3E−10  0/31 N sigma factor SigA Naga_100146g3 Fungal Zn(2)-Cys(6) binuclear −1.6 1.7E−02 24/31 Y cluster domain Naga_101321g2 Zinc finger, CCCH-type −1.5 4.5E−03  9/30 Y Naga_100489g1 Zinc finger, TAZ-type −1.4 3.6E−05 1/6 Y Naga_100042g29 SANT/Myb domain protein −1.4 1.1E−03 17/32 Y Naga_100248g8 Winged helix-turn-helix −1.3 3.1E−04  3/23 Y transcription repressor DNA- binding Naga_100066g21 CCT motif family protein −1.3 9.6E−06  5/30 Y Naga_100084g18 Myb-like DNA-binding shaqkyf −1.2 8.6E−06 17/32 Y class family protein Naga_100339g1 Nucleic acid-binding protein −1.2 1.6E−04 0/8 N Naga_100087g2 Activating transcription factor 6 −1.1 9.0E−05 16/29 Y Naga_100249g5 Fungal Zn(2)-Cys(6) binuclear −1.1 4.1E−06 19/31 Y cluster domain Naga_100329g4 Fungal specific transcription factor −1.1 9.1E−04 14/31 Y domain-containing region Naga_100028g52 Zn(2)-C6 fungal-type transcription −0.9 2.5E−03 10/31 Y factor Naga_100019g66 Winged helix-turn-helix −0.9 1.1E−03 22/31 Y transcription repressor Naga_100146g5 Fungal Zn(2)-Cys(6) binuclear −0.9 9.9E−04 14/31 Y cluster domain Naga_100086g13 Myb-like dna-binding domain −0.9 7.7E−04 25/32 Y containing protein Naga_100001g82 Fungal Zn(2)-Cys(6) binuclear −0.9 3.6E−03 2/32 Y cluster domain Naga_100001g77 Aureochrome1-like protein −0.5 3.9E−02 16/32 Y ^(†)FDR, False discovery rate ^(††)Y, successful insertion of the selection cassette; N, unsuccessful insertion, as determined by PCR genotyping

Example 2 Knockout of Transcription Factor Genes in Nannochloropsis

All 20 transcription factor genes that were discovered to be differentially regulated under nitrogen deprivation (Table 1) were targeted for insertional knockout mutagenesis via the development of a high-efficiency Cas9-expressing editor line in Nannochloropsis (see WO 2016/109840 and corresponding U.S. application Ser. No. 14/986,492, filed Dec. 31, 2015, incorporated herein by reference in its entirety). As described in U.S. Ser. No. 14/986,492, a highly efficient Nannochloropsis Cas9 Editor line, N. gaditana strain GE-6791, expressing a gene encoding the Streptococcus pyogenes Cas9 nuclease, was used as a host for transformation with a chimeric guide RNA and donor DNA for insertional knockout.

To produce the high efficiency Nannochloropsis Cas9 Editor line, a Nannochloropsis strain was engineered and isolated that exhibited expression of the introduced cas9 gene in essentially 100% of the cell population of a growing culture. The vector pSGE-6206 (FIG. 2; SEQ ID NO:26), used to transform wild type N. gaditana strain WT-3730 included the following three elements: 1) a Cas9 expression cassette which contained a Cas9 gene from Streptococcus pyogenes codon optimized for Nannochloropsis gaditana (SEQ ID NO:27) that also included sequences encoding an N-terminal FLAG tag (SEQ ID NO:28), nuclear localization signal (SEQ ID NO:29), and peptide linker (entire FLAG, NLS, and linker sequence provided as SEQ ID NO:30), driven by the N. gaditana RPL24 promoter (SEQ ID NO:31) and terminated by N. gaditana bidirectional terminator 2 or “FRD” terminator (SEQ ID NO:32); 2) a selectable marker expression cassette, which contained the blasticidin deaminase (“blast” or “BSD”) gene from Aspergillus terreus codon optimized for N. gaditana (SEQ ID NO:33), driven by the N. gaditana TCTP promoter (SEQ ID NO:34) and followed by the EIF3 terminator (SEQ ID NO:35); and 3) a GFP reporter expression cassette, which contained the TurboGFP gene (Evrogen, Moscow, Russia) codon optimized for Nannochloropsis gaditana (SEQ ID NO:36), driven by the N. gaditana 4A-III promoter (SEQ ID NO:37) and followed by the N. gaditana bidirectional terminator 5 or “GNPDA” terminator (SEQ ID NO:38). The Cas9 expression construct was assembled according to the Gibson Assembly® HiFi 1 Step Kit (Synthetic Genomics, La Jolla, Calif.) into a minimal pUC vector backbone; the confirmed DNA sequence of this plasmid is provided as SEQ ID NO:26.

The ZraI-linearized Cas9 expression construct (FIG. 3A) was transformed into Nannochloropsis cells by electroporation. 1×10⁹ cells were transformed in a 0.2 cm cuvette using a field strength of 7,000 V/cm delivered with the Gene Pulser II (Biorad, Carlsbad, Calif., USA). The transformation mixture was plated onto PM074 agar medium containing 100 mg/L of blasticidin. Resulting colonies were patched onto selection media for analysis and archiving. A small amount of biomass was taken from the patches and completely resuspended in 300 μl of 1× Instant Ocean Salts solution (Aquatic Eco Systems; Apopka, Fla.). Care was taken to not add too much biomass so that a light green resuspension was obtained. This suspension was directly analyzed by flow cytometry using a BD Accuri C6 flow cytometer, using a 488 nm laser and 530/10 nm filter to measure GFP fluorescence per cell. 10,000-30,000 events were recorded for each sample using the slow fluidics setting. A strain having a single fluorescence peak that was shifted to a fluorescence level higher than that demonstrated by wild-type cells (FIG. 3B) and also demonstrating cas9 protein expression by Western blotting using an anti-FLAG antibody (Sigma #A9469) (FIG. 3C), designated strain GE-6791, was selected as a cas9 Editor strain and used in mutant generation by cas9/CRISPR genome editing as described herein. The Ng-Cas9 Editor line was found to be equivalent to wild-type in FAME and TOC productivity (see for example FIG. 18).

Generation of Targeted Insertional Mutants in the Ng-Cas9 Editor Line

All 20 identified transcription factors that were found to be downregulated under nitrogen starvation (Table 1) were targeted for knockout in the Cas9 Editor line. Guide RNAs (see Table 2 for the target sequences used for knockout of each of the 23 transcription factors) were synthesized in vitro according to (Cho et al. (2013) Nature Biotechnol. 31: 230-232) and described in Example 3, and co-electroporated with a PCR amplified expression cassette (pHygR, SEQ ID NO:45) containing a codon optimized hygromycin resistance gene (HygR, SEQ ID NO:44) driven by endogenous the EIF3_promoter (SEQ ID NO:46) and followed by N. gaditana NADH-dependent fumarate reductase bidirectional terminator (SEQ ID NO:32) in inverted orientation. Approximately 1 μg each of the guide RNA targeting the particular transcription factor and the pHygR donor fragment (FIG. 4A) were added to the cuvette and electroporation was performed as described above. In general, loss-of-function “knockout” mutants were generated by selecting a guide RNA target locus in the first half of exonic coding sequence. Selection of HygR transformants was as above except that 500 mg/L hygromycin was added to agar plates instead of blasticidin. Targeted insertion of the pHygR fragment via NHEJ-mediated repair of the double stranded DNA break catalyzed by Cas9 in loci targeted by guide RNAs was assessed by colony PCR using primers that flanked the guide RNA target site by ˜200 bp on either side (Table 3). Using these primers, PCR amplification of wild-type loci would result in ˜400 bp products, whereas pHygR targeted insertional mutants would result in ˜2800 bp products—accounting for the insertion of the 2400 bp pHygR fragment. PCR products were sequence-confirmed for all mutants allowing for the determination of insert orientation and detection of any loss of chromosomal and/or insert DNA, or the gain of small insertions generated during the NHEJ-mediated dsDNA break repair process (see FIGS. 4B and 4C for a diagram of the insertion process and exemplary colony PCR results).

Eighteen of the 20 targeted transcription factors (Table 1) were disrupted at the intended locus as confirmed by PCR genotyping. Based on the high overall editing efficiency observed it is likely that the remaining 2 loci were essential for viability. To test the knockouts for effects on lipid induction, two independent mutants per locus were screened for lipid and biomass productivities by assessing FAME and TOC levels throughout multiple time-points of a 7-day culture as described in detail in Example 4, below.

TABLE 2 Guide RNA Sequences and Screening Primers Used in Cas9-Mediated Mutagenesis Target Sequence N. gaditana id Description Adjacent to PAM (NGG) Naga_100055g29 CCT domain protein TTCCGAAGTACTGGTTC (SEQ ID NO: 87) Naga_100104g18 Zn(2)-C6 fungal-type DNA-binding domain AGTAGGCCATTCCCGGAG protein (ZnCys-2845) (SEQ ID NO: 88) Naga_100489g1 Zinc finger, TAZ-type TGTGGCAGACGCCGACGG (SEQ ID NO: 89) Naga_100043g41 RpoD family RNA polymerase sigma factor SigA GTACTGCCTGACAAACTAGG (SEQ ID NO: 90) Naga_100146g3 Fungal Zn(2)-Cys(6) binuclear cluster domain TGAGCAGTCGTACGAAA (SEQ ID NO: 91) Naga_101321g2 Zinc finger, CCCH-type CGAAGTCAACCATGGGGC (SEQ ID NO: 92) Naga_100248g8 Winged helix-turn-helix transcription repressor TCCTGTGACTTGACGGTG DNA-binding (SEQ ID NO: 93) Naga_100042g29 SANT/Myb domain protein GGCAATACAAGCAGTGGAAG (SEQ ID NO: 94) Naga_100066g21 CCT motif family protein CTGATCTCGAGATGGCTG (SEQ ID NO: 95) Naga_100329g4 Fungal specific transcription factor domain- GTGAAGATTGGTCCCACT containing protein (SEQ ID NO: 96) Naga_100084g18 Myb-like DNA-binding shaqkyf class family GGACGCTACGACCGTGCGGG protein (SEQ ID NO: 97) Naga_100339g1 Nucleic acid-binding protein CTGCACCAGACACAAATT (SEQ ID NO: 98) Naga_100087g2 Activating transcription factor 6 GGGAAATATTAAGACTGGAG (SEQ ID NO: 99) Naga_100249g5 Fungal Zn(2)-Cys(6) binuclear cluster domain TCACGGGAGATGTCCTGT (SEQ ID NO: 100) Naga_100028g52 Zn(2)-C6 fungal-type transcription factor AGGACTCTCCTCAGCTGA (SEQ ID NO: 101) Naga_100019g66 Winged helix-turn-helix transcription repressor TCTTCATCTGCGACAACG (SEQ ID NO: 102) Naga_100146g5 Fungal Zn(2)-Cys(6) binuclear cluster domain ACGTCCGAATATACCGAA (SEQ ID NO: 103) Naga_100086g13 Myb-like dna-binding domain containing protein GTAGAACAAGCGTTAGACC (SEQ ID NO: 104) Naga_100001g82 Fungal Zn(2)-Cys(6) binuclear cluster domain CGCCACCCTCGCACGTGTC (SEQ ID NO: 105) Naga_100001g77 Aureochromel-like protein GGCACCATCCCCACCGGTTT (SEQ ID NO: 106) Naga_100104g18 ZnCys-2845 (Guide targets 5′UTR resulting in GGGACTGTCCCATTGTGC strain ZnCys-2845 BASH-3) (SEQ ID NO: 54) Naga_100104g18 ZnCys-2845 (Guide targets 3′UTR resulting in AACTCGCTCGTCGATCAC strain ZnCys-2845 BASH-12) (SEQ ID NO: 62) Naga_100699g1 Nitrate Reductase GGGTTGGATGGAAAAAGGCA (SEQ ID NO: 193)

TABLE 3 Screening Primers Used in Cas9-Mediated Mutagenesis N. gaditana id Genotyping Primer (Sense) Genotyping Primer (Antisense) Naga_100055g29 AAGTGCGCAAGACGCTCCAG TTTGAATATCTGCACATGCA (SEQ ID NO: 107) (SEQ ID NO: 108) Naga_100104g18 ACCTCCTTGTCACTGAGCAG GATCCCAAAGGTCATATCCGT ZnCys-2845 (SEQ ID NO: 109) (SEQ ID NO: 110) Naga_100489g1 ACTCTGTGCTACCAATTGCTG CGTCAGCAAATCTTGCACCA (SEQ ID NO: 111) (SEQ ID NO: 112) Naga_100043g41 GAGATGCTGTCCGAGACACG GTATCTCGGACAGGGCACTG (SEQ ID NO: 113) (SEQ ID NO: 114) Naga_100146g3 ATCCATGTAAAGACGATGTGC TGATATCACATGCTCAAGGTC (SEQ ID NO: 115) (SEQ ID NO: 116) Naga_101321g2 AGATGAGGATCAAGCACCGAGCCA GGAAGAAATAGTAGTTGCGTG (SEQ ID NO: 117) (SEQ ID NO: 118) Naga_100248g8 AGGCGCTCTGATTGCTGTGGC TCTTCCACGTCGGATGGCCAG (SEQ ID NO: 119) (SEQ ID NO: 120) Naga_100042g29 ATTGTGGAGGGTAACAAACTACG TGAGTCCCGTGGAGAGGAGTCG (SEQ ID NO: 121) (SEQ ID NO: 122) Naga_100066g21 AGGTTCCAATGGAGGCCGCA CACTTTCCTTCGTACGCTCAGC (SEQ ID NO: 123) (SEQ ID NO: 124) Naga_100329g4 CTCGAGGTAGGTGGTGAAAG GTGATTCGCATGGACGAAC (SEQ ID NO: 125) (SEQ ID NO: 126) Naga_100084g18 ATGGGTACGGACTTGTTCG ACAGCGATACGGACAGTGAC (SEQ ID NO: 127) (SEQ ID NO: 128) Naga_100339g1 GACGTTGCATGAGAAAGGAG GATGCACAGGTGCTTGTTAG (SEQ ID NO: 129) (SEQ ID NO: 130) Naga_100087g2 TGCAAAGCCTATTTCCGACG CTCATTCGTGAGGTGACCAT (SEQ ID NO: 131) (SEQ ID NO: 132) Naga_100249g5 GAGCAAACTGACATTGATAC GTACCACACATACACATG (SEQ ID NO: 133) (SEQ ID NO: 134) Naga_100028g52 CACATCCACCATCATTCCAC GAGTGTTCCCAGTGAGCCAG (SEQ ID NO: 135) (SEQ ID NO: 136) Naga_100019g66 CTGACAAGAAGATGGACATG CTTTAGTTATACGTCTGAAG (SEQ ID NO: 137) (SEQ ID NO: 138) Naga_100146g5 GAGAGGATAGTTCTCAGAG GTCCCACAATCTATTGTG (SEQ ID NO: 139) (SEQ ID NO: 140) Naga_100086g13 ATGAGTACTTGCGCGCTTTG GCATGCCTCCGTCACAGAGT (SEQ ID NO: 141) (SEQ ID NO: 142) Naga_100001g82 ATCCATTGAGCATGCCGACG GCAACATGTTAATGCATCGT (SEQ ID NO: 143) (SEQ ID NO: 144) Naga_100001g77 TCGTCCTCGAACTCTTCCTC CGGGAACAACCAAGGTGTAA (SEQ ID NO: 145) (SEQ ID NO: 146) Naga_100104g18 TAGCAGAGCAGGCTCATCAC GAATATGTGGTCTAGCTCGT ZnCys-2845 (SEQ ID NO: 147) (SEQ ID NO: 148) BASH-3 Naga_100104g18 ATGGCTCCACCCTCTGTAAG CTGACTACAGCTAGCACGAT ZnCys-2845 (SEQ ID NO: 149) (SEQ ID NO: 150) BASH-12 Naga_100699g1 AAGACTTTGGAGGATGTCTGAGTGG ACGAAGCTACATCCAGTGCAAGG (SEQ ID NO: 151) (SEQ ID NO: 152)

Example 3 ZnCys-2845 Knockout Mutant

The ZnCys-2845 gene (Naga_100104 g18, second row of Table 1) was targeted for disruption by first making a DNA construct for producing a guide RNA in which the construct included the sequence of a chimeric guide engineered downstream of a T7 promoter. The chimeric guide sequence included an 18 bp target sequence (SEQ ID NO:39) homologous to a sequence within the ZnCys-2845 gene sequence that was immediately upstream of an S. pyogenes cas9 PAM sequence (NGG), and also included the transactivating CRISPR (tracr) sequence. The chimeric guide sequence was synthesized by first making a DNA template made up of complementary DNA oligonucleotides that included the T7 promoter sequence (SEQ ID NO:40 and SEQ ID NO:41, made by SGI-DNA, La Jolla, Calif.) that incorporated the T7 promoter sequence and were annealed to create a double-stranded DNA template which was used in in vitro transcription reactions using the MEGAshortscript™ T7 Kit (Life Technologies #AM1354M) according to the manufacturer's instructions to synthesize the guide RNA. The resulting RNA was purified using Zymo-Spin™ V-E columns (Zymo Research #C1024-25) according to manufacturer's protocol.

The donor fragment for insertion into the targeted ZnCys-2845 locus (SEQ ID NO:44) included a selectable marker cassette that included the hygromycin resistance gene (HygR, SEQ ID NO:45) downstream of the N. gaditana EIF3 promoter (SEQ ID NO:46) and followed by N. gaditana bidirectional terminator 2 (SEQ ID NO:32), with the entire promoter-hygromycin resistance gene-terminator sequence flanked by 27 base pair identification sequences on the 5′ (SEQ ID NO:47 5′ID) and 3′ (SEQ ID NO:48 3′ID) ends to yield the DNA fragment referred to as the “Hyg Resistance Cassette” (SEQ ID NO:44, HygR Cassette).

For targeted knockout of the ZnCys-2845 (Naga_100104 g18) locus, Cas9 Editor line GE-6791 was transformed by electroporation using 5 μg of purified chimeric guide RNA targeting the ZnCys-2845 gene and 1 μg of the selectable donor DNA (Hyg Resistance Cassette; SEQ ID NO:44, shown in FIG. 4A) essentially as described in US 2014/0220638. Following electroporation, cells were plated on PM124 agar media containing hygromycin to select for transformants that incorporated the hygromycin resistance cassette. Transformants were patched onto a fresh plate and screened by colony PCR for insertion of the donor fragment into the ZnCys-2845 gene.

For colony PCR screening, a small amount of cells from a colony to be screened was suspended into 100 μl of 5% Chelex 100 Resin (BioRad)/TE solution and the suspension was boiled for 10 minutes at 99° C., after which the tubes were briefly spun. One microliter of the lysate supernatant was added to a PCR reaction mix, in which the PCR mixture and reactions were set up and performed according to the QIAGEN Fast Cycling PCR Master Mix Protocol from the manufacturer (Handbook available at qiagen.com). The primers used to detect the insertion of the donor fragment into the targeted locus of the ZnCys-2845 gene were SEQ ID NO:49 and SEQ ID NO:50. Based on the PCR-based colony screening, two knockout strains, GE-8564 and GE-8565, were tested in productivity assays.

As described below, mutants harboring the HygR cassette in the coding sequence of genome locus Naga_100104 g18 had an insertion of the donor cassette in a gene encoding a predicted Zn(II)2Cys6 binuclear cluster domain protein (Pfam PF00173, see FIG. 5) and is referred to as ZnCys-2845. These mutants exhibited a marked increase in lipid accumulation with respect to wild type as assessed by FAME/TOC (Example 4, FIG. 7C). As described below, the lipid accumulation phenotype in these ZnCys-2845 KO mutants was further confirmed to be similar to that observed in nitrogen-starved wild type cells by the appearance of prominent lipid droplets (FIGS. 7 F-H).

Example 4 ZnCys-2845 Knockout Mutants in Batch Productivity Assay

To determine the effect of knocking out the ZnCys-2845 gene on growth and lipid production, ZnCys-2845 knockout strain GE-8564 and the wild type progenitor strain WT-3730 were cultured in a batch productivity assay in nitrogen replete medium PM123 that included 15 mM nitrate as the sole nitrogen source available to the cells, i.e., the culture medium had no source of reduced nitrogen. Because it had been determined that the ZnCys-2845 mutant does not grow in the absence of reduced nitrogen, the production cultures were inoculated to an initial OD730 of 0.5 from seed (scale-up) cultures that were grown in PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate.

After inoculation, ZnCys knockout strain GE-8564 and wild type strain WT-3730 were grown in triplicate cultures in a batch assay in 75 cm² rectangular tissue culture flasks containing 175 ml of PM123 medium, which includes 15 mM nitrate as the sole nitrogen source, for seven days. The flasks were positioned with their narrowest “width” dimension against an LED light. The culture flasks were masked with an opaque white plastic to provide a 21.1 cm² rectangular opening for irradiance to reach the cultures. Incident irradiance was programmed at a 16 h light: 8 hour dark cycle with a linear ramp up of irradiance from 0 to 1200 uE over 4 hours, after which the irradiance was held at for six hours at 1200 uE, and then a linear ramp down in irradiance from 1200 to 0 uE over a 4 h period (increasing in 15 min intervals) (FIG. 6A). Deionized H₂O was added to the cultures daily to replace evaporative losses. The temperature of the cultures was regulated by a water bath set at 25° C. Cultures were inoculated at OD730 of 0.5 on day 0 and samples (5 mls) were removed on days 3, 5, and 7 for assessing cell density, fatty acid methyl esters (FAME) as a measure of lipid, and total organic carbon (TOC). Sampling was done 30 minutes prior to the end of the light cycle. FAME analysis was performed on 2 mL samples that were dried using a GeneVac HT-4X. To each of the the dried pellets the following were added: 500 μL of 500 mM KOH in methanol, 200 μL of tetrahydrofuran containing 0.05% butylated hydroxyl toluene, 40 μL of a 2 mg/ml C11:0 free fatty acid/C13:0 triglyceride/C23:0 fatty acid methyl ester internal standard mix and 500 μL of glass beads (425-600 μm diameter). The vials were capped with open top PTFE septa-lined caps and placed in an SPEX GenoGrinder at 1.65 krpm for 7.5 minutes. The samples were then heated at 80° C. for five minutes and allowed to cool. For derivatization, 500 μL of 10% boron trifluoride in methanol was added to the samples prior to heating at 80° C. for 30 minutes. The tubes were allowed to cool prior to adding 2 mL of heptane and 500 μL of 5 M NaCl. The samples were vortexed for five minutes at 2K rpm and finally centrifuged for three minutes at 1K rpm. The heptane layer was sampled using a Gerstel MPS Autosampler. Quantitation used the 80 μg of C23:0 FAME internal standard. The samples were run on an Agilent 7890A gas chromatography system using an Agilent 127-3212 DB-FFAP, 10 m×100 m×100 nm column and an FID detector at 260° C. The flow rate was 500 μL/minute using H₂ as a carrier with constant flow control. The oven was set at 90° C. for 0.98 min, then 15.301° C./minute to 230° C. and held for 1.66 min. The inlet contained a 4 mm glass wool packed liner (Agilent P/N 5183-4647), and was set at 250° C. and used a split ratio of 40:1. The injection volume was 900 nL.

Total organic carbon (TOC) was determined by diluting 2 mL of cell culture to a total volume of 20 mL with DI water. Three inj ections per measurement were injected into a Shimadzu TOC-Vcsj Analyzer for determination of Total Carbon (TC) and Total Inorganic Carbon (TIC). The combustion furnace was set to 720° C., and TOC was determined by subtracting TIC from TC. The 4 point calibration range was from 2 ppm to 200 ppm corresponding to 20-2000 ppm for non-diluted cultures with a correlation coefficient of r²>0.999.

The results of these analyses are shown in Tables 4-6. Values provided for wild type and knockout GE-8564 mutant are the average of three cultures with standard deviations (sd). The “% increase” column refers to the percentage increase of the ZnCys knockout mutant with respect to wild type values.

TABLE 4 Lipid (FAME) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO₃) Day μg/ml sd μg/ml sd % increase 3 105.03 9.71 188.56 6.52 79.53 5 140.01 13.48 223.41 0.28 59.57 7 198.49 2.04 250.76 3.22 26.33

TABLE 5 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO3) Day μg/ml s.d. μg/ml s.d. % diff 3 375.6 10.18 261.7 7.07 −30.3 4 474.6 8.34 283.95 3.61 −40.2 5 534.45 43.20 269.5 3.68 −49.6 6 644.8 48.65 311.75 3.18 −51.7 7 804.35 36.13 329.3 1.70 −59.1

TABLE 6 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild Type Strains in Batch Assay with Nitrate-Only Culture Medium WT-3730 (NO3) ZnCys-KO GE-8564 (NO3) Day s.d. s.d. % increase 3 0.28 0.018 0.72 0.044 157 5 0.26 0.004 0.83 0.012 219 7 0.25 0.009 0.76 0.006 204

The same batch productivity assay was performed on ZnCys-2845 cas9 knockout mutant GE-8564 using PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate. Samples were removed as described and analyzed for FAME and TOC as provided above. The “% difference” column refers to the percentage difference of the ZnCys knockout mutant with respect to wild type values.

TABLE 7 FAME Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 ZnCys-KO GE-8564 (NO3 + NH4) (NO3 + NH4) DAY μg/ml s.d. μg/ml s.d. % diff 3 93.03 6.943 88.43 1.827 −4.9 4 120.14 8.427 124.41 0.472 3.6 5 121.31 0.7895 123.31 3.702 1.6 6 169.70 6.0668 181.6 3.397 7.0 7 198.11 7.954 225.6 4.548 13.88

TABLE 8 Biomass (TOC) Produced by ZnCys-2845 Knockout Mutant and Wild Type Cultures in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 ZnCys-KO GE-8564 (NO3 + NH4) (NO3 + NH4) DAY μg/ml s.d. μg/ml s.d. % diff 3 321.5 35.07 302.7 6.36 −5.8 4 392.3 16.69 415.65 11.10 6.0 5 464 4.384 502.3 5.80 8.3 6 556.45 20.15 637.65 14.21 14.59 7 679.95 6.01 728.6 32.10 7.15

TABLE 9 FAME/TOC Ratios of ZnCys-2845 Knockout Mutant and Wild Type Strains in Batch Assay with Nitrate Plus Ammonium Culture Medium WT-3730 ZnCys-KO GE-8564 (NO3 + NH4) (NO3 + NH4) Day s.d. s.d. % diff 3 0.29 0.0100 0.29 0.0001 0 4 0.31 0.0085 0.30 0.0091 −3.2 5 0.26 0.0008 0.25 0.0045 −3.8 6 0.31 0.0220 0.29 0.0117 −6.5 7 0.29 0.0091 0.31 0.0074 6.9

The graphs in FIGS. 7A-7D show the results of this analysis. FIG. 7A demonstrates that cultures of ZnCys-2845 knockout strain GE-8564 (average values for triplicate cultures depicted as circles on the graph) grown in a medium that included only nitrate as a nitrogen source had higher FAME content than wild type cultures every day tested. As can be seen in Table 4, these FAME values were considerably higher than wild type on a volumetric basis. Although the FAME content of the ZnCys-2845 knockout mutant culture in nitrate-only medium was at a higher level on day 3 of the culture, which was the first day assayed, as well as on days 5 and 7 (Table 4 and FIG. 7A), the increase in FAME per day between days 3 and 7 was less for the ZnCys-2845 knockout strain than for the wild type strain. FIG. 7B demonstrates that over this time period the ZnCys-2845 gene disruption mutant cultured in nitrate-only medium (circles) increased its total organic carbon very little as compared to wild type (Xs), which showed steady growth as assessed by TOC accumulation (as also seen in Table 5). Thus, the ZnCys-2845 knockout strain, when cultured in a medium that included nitrate as the sole nitrogen source, behaved as though it were in nitrogen starvation, increasing lipid production but also decreasing in biomass accumulation. FIG. 7C confirms this, demonstrating that over the course of the one week productivity assay, the FAME/TOC ratio of the ZnCys-2845 knockout strain GE-8564 was elevated over wild type (approximately three-fold that of wild type, Table 6), with greater than 60% (and up to at least about 80%) of TOC being allocated to FAME lipids. FIG. 7D shows that the C16 and C18 fatty acids that were overproduced in knockout strain GE-8564 (black bars) with respect to wild type in nitrogen replete conditions (diagonally striped bars), while C20 fatty acids were underrepresented with respect to their abundance in wild type cells, as expected for selective overproduction of storage lipids (i.e., triglycerides). The fatty acid profile of the GE-8564 knockout strain was very similar to that of wild type cells under nitrogen starvation (dotted bars).

Direct demonstration of TAG production was determined by analysis of extracted lipids. Extracted lipids of knockout mutant GE-8564 and wild type progenitor strain WT-3730 from samples taken on Day 7 of the batch assay in the nitrate-only PM074 medium were identified and quantitated by HPLC. For HPLC analysis of lipids, 2 mL samples of each culture were spun down at maximum speed for 5 minutes, the supernatants were removed, and pellets were re-suspended in 400 μL of H₂O. The cell suspensions (approximately 500 μL) were transferred to 4 mL glass vials with Teflon lined caps. 500 μL of glass beads (212-300 μm diameter) were added to each of the cell suspensions, after which 50 μL of 50% H₂SO₄ and 100 μL of 5M NaCl were added. Bead beating was performed for 5 minutes at 1 krpm, then 2 mL of hexane was added to each sample, and bead beating was repeated for 5 minutes at 1 krpm. The samples were loaded onto a multi-tube vortexer and shaken for 30 minutes at 1 krpm, and then vortexed for 30 seconds at 2.5 krpm. 500 μL of the organic layer was transferred to an HPLC vial, and 50 μL of internal standard solution (1 mg/mL 6-ketocholestanol in toluene) was added to each vial. Standards were from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped and vortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. The HPLC was run at a flow rate of 2 mL/minute on a Chromegasphere SI-60 150 mm×4.6 mm×10 μm column (ES Industries), with a column compartment set at 40° C. The injection volume was 25 μL with a draw and eject speed of 200 μL/minute. Eluent A was hexane and Eluent B was a 80:10:10:1 mixture of hexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol, run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min; 25% B at 5.0 min; 98% B at 5.5 min; 98% B at 8.99 min; 2% B at 9.00 min; stop time: 9.0 minutes; 4 minutes post time. The detector was ELSD at 30° C. and 3.5 bar N₂, with a gain of 5.

FIG. 7E shows that the amount of TAG in the ZnCys-2845 knockout cells in nitrate only medium was more than 5-fold that of the wild type cells, that is, the observed increase in FAME lipid could be attributed to the increase in TAGs. Electron microscopy also showed the dramatic lipid accumulation characteristic of the nitrogen starvation response. FIG. 7F shows a wild type cell grown under nitrogen replete conditions (nitrate-only culture medium), with a prominent nucleus (N), chloroplast (Ch), and mitochondrion (M), as well as a few small lipid droplets (LD). FIG. 7G shows the ZnCys knockout mutant grown in nitrate-only medium, in which a prominent lipid droplet (LD) is the largest cellular structure visible, a cellular morphology highly similar to the nitrogen starved wild type cell shown in FIG. 7H. Thus, the ZnCys-2845 polypeptide acts as a negative regulator of lipid biosynthesis, as attenuating expression of the ZnCys-2845 gene results in increased lipid production.

The increase in FAME exhibited by the ZnCys-2845 knockout strain cultured in nitrate-only medium was not apparent when the ZnCys-2845 knockout strain was grown in a culture medium that also included ammonium however (Table 7). In this case, the amount of FAME produced was very similar to that produced by wild type cells grown in nitrate plus ammonium medium, with lipid production of the knockout mutant increasing somewhat relative to wild type toward the end in the run, probably indicating depletion of ammonium from the batch culture (Table 7). FIG. 8A shows that the amount of FAME produced by wild type (diamonds) and the ZnCys-2845 knockout strain (circles) cultured in ammonium-only medium was virtually identical over the one week batch assay, as was TOC accumulation, shown in FIG. 8B (also evident from Table 8). FAME/TOC values of the wild-type and ZnCys-2845 knockout strain were correspondingly similar (FIG. 8C, Table 9).

Thus, the ZnCys-2845 gene disruption mutant behaved like the wild type strain when ammonium was replete in the culture medium (Tables 7-9 and FIGS. 8A-8C), but appeared to be impaired in nitrate assimilation, behaving as though the cells were in nitrogen depleted medium when nitrate was the sole source of nitrogen present by inducing storage lipid biosynthesis (FIGS. 7A-7H).

Example 5 Bioinformatic Analysis of the ZnCys-2845 Protein: Domains and Orthologs

As described in Example 1, the ZnCys-2845 gene at locus Naga 100104 g18 that was differentially expressed between the N-replete and N-deplete samples was a gene (cDNA sequence provided as SEQ ID NO: 1) encoding a polypeptide (SEQ ID NO:2) that appeared on a bioinformatics-generated Nannochloropsis putative transcription factor list. The polypeptide was observed to have a Zinc(2)Cys(6) domain characteristic of some transcription factors and is therefore classified as a Zn(2)-C(6) fungal-type DNA-binding domain protein. In addition to the Zn(2)-Cys(6) domain, the Nannochloropsis polypeptide ZnCys-2845 contains a distinct nuclear localization sequence with a confidence score of 1.0 (which equates to 100% confidence), consistent with its characterization as transcription factor (FIG. 5).

ZnCys-2845 is a 1065 amino acid protein (SEQ ID NO:2) identified by transcriptomics analysis of genes differentially regulated during lipid induction and annotated as a putative transcription factor due to the Zn(2)-Cys(6) binuclear cluster domain extending from amino acid 190 to 219 (SEQ ID NO:3). The protein recruits to Pfam PF00172 (“Zn_Clus” or “Fungal Zn(2)-Cys(6) binuclear cluster domain” with a bit score of 25.2 (the gathering cutoff for this family is 20.8) and an e value of 1.1 e-05. Thus, ZnCys-2845 is a member of the Zn(II)2Cys6 fungal-type DNA-binding domain protein family. Members of this family contain the well-conserved motif CysX₂CysX₆CysX₅₋₁₂CysX₂CysX₆₋₈Cys (a cysteine residue followed by two amino acid residues of any identity, followed by second cysteine residue followed by six amino acid residues of any identity, followed by a third cysteine residue followed by between five and twelve amino acid residues of any identity, followed by a fourth cysteine residue followed by two amino acid residues of any identity, followed by a fifth cysteine residue followed by between six and eight amino acid residues of any identity, followed by a sixth cysteine residue; SEQ ID NO:4). It has been demonstrated that the cysteine residues can bind two zinc atoms, which coordinate folding of the domain involved in DNA binding. Other identifiers for this domain include the conserved domain database (cdd) domain cd00067, the interpro protein domain database domain IPR001138, the SMART protein domain ‘GAL4’, and the PROSITE protein domain PS00463.

This class of “ZnCys” transcription factors was originally thought to be exclusively fungal, but more recently members have been identified among chromalveolates, in particular stramenopiles/heterokonts (including non-photosynthetic labyrinthulomycetes or “chytrids”) and haptophytes (e.g., E. huxleyi). The first and best studied protein in this family is Gal4p, a Saccharomyces transcriptional activator of genes involved in galactose catabolism (Leverentz & Reece (2006) Biochem Soc Transac 34:794-797; Breunig (2000) Food Technol. Biotechnol. 38:287-293). The terms “Zn(2)-C(6) fungal-type DNA-binding domain protein”, “Zn(II)2Cys6 fungal-type DNA-binding domain protein”, “Zn(2)-Cys(6) domain polypeptide”, “Zn(2)Cys(6) protein/polypeptide” and “Zn2Cys6 protein/polypeptide” are used interchangeably herein.

Examination of genome databases revealed genes encoding polypeptides having Zn(2)-Cys(6) domains in plants and fungi. Interestingly, several heterokont species were found to include Zn(2)-Cys(6) domain polypeptides, including labyrinthulomycete species such as from the genera Schizochytrium and Aplanochytrium and diatom species, including members of the Navicula, Cyclotella, Thalassiosira, Phaeodactylum, Fragilariopsis genera.

TABLE 10 Putative Orthologs of N. gaditana Lipid Regulator ZnCys-2845 SEQ Translation ID Species Library ID NO Phaeodactylum triconutum Phatr2_2 337562 5 Navicula sp. wt0229_cDNA_clc 4242909 6 Navicula sp. wt0229_cDNA_clc 4243087 7 Navicula sp. wt0229_cDNA_clc 4238609 8 Cyclotella sp. wt0293_nuclear_v1.3 5077789 9 Cyclotella sp. wt0293_nuclear_v1.3 5083384 10 Cyclotella sp. wt0293_nuclear_v1.3 5084316 11 Thalassiosira pseudonana thaps3_2 322124 12 Thalassiosira pseudonana thaps3_2 326683 13 Thalassiosira pseudonana thaps3_2 326937 14 Fragilariopsis cylindrus fracy1_2 386612 15 Fragilariopsis cylindrus fracy1_2 386837 16 Nannochloropsis oceanica Wt-5473 17

The N. oceanica gene (coding sequence provided as SEQ ID NO:84, encoded polypeptide provided as SEQ ID NO: 17) was found by scanning the predicted protein set of a proprietary Nannochloropsis genome for matches to the PF00172 HMM model using hmmsearch (hmmer.org) and the trusted cutoff for the match score; however, no additional Nannochloropsis orthologs were found by scanning Nannochloropsis genomes downloaded from singlecellcenter.org/en/NannoRegulationDatabase/Download/S 11.zip, probably due to incomplete protein sets of the genomes. Additional putative orthologs of the Nannochloropsis gaditana ZnCys-2845 protein (SEQ ID NO:2) were found by BLAST (tblastn) against public genome assemblies of Nannochloropsis strains and species, including N. gaditana strain CCMP526, N. oceanica strain IMET1, N. oceanica strain CCMP531, N. oculata strain CCMP525, N. salina strain CCMP537, and N. granulata strain CCMP529. However, in each case the alignment matches were observed to break within the PF00172 Zn_Clus domain, such that all of the sequences were found to be incomplete, lacking the 5′ end of the coding region and N-terminal sequence of the proteins. An additional conserved region, approximately 170 amino acids in length from the ZnCys-2845 polypeptide (positions 345-51 of SEQ ID NO:27), was clearly identified in all Nannochloropsis genomes analyzed and examined further. The delta-blast tool in NCBI was used to evaluate the highly conserved region between N. gaditana WT-3730 ZnCys-2845 (SEQ ID NO:2) putative orthologs in other Nannochloropsis species.

This domain, a PAS3_fold domain (pfam PF08447), is found in many signaling proteins where it functions as a signal sensor. Using this approach putative matches to ZnCys-28345 could be clearly identified in each of the six Nannochloropsis genomes searched. Unfortunately, the alignment matches in all cases appeared to break within the putative match to the PF00172 Zn_Clus domain. However, from the blast alignments, an approximately 170 aa region from ZnCys-28345 (positions 345-517) was observed and clearly identifiable across all strains (single copy). An alignment of the PAS3 domains in the identified ZnCys-2845 orthologs from Nannochloropsis is provided in FIG. 9, where the high degree of conservation of the domain sequence among different Nannochloropsis species is evident. The PAS3 domain of ZnCys-2845 (identified in the gene diagram of FIG. 12A) extends from amino acid 345 to amino acid 517 of SEQ ID NO:2, and is provided as SEQ ID NO:21. SEQ ID NO:21 also represents the sequence of the PAS3 domain of N. gaditana strain CCMP526. The sequence of the PAS3 domain of N. oceanica strain WT-5473, N. oceanica strain IMET1, and N. oceanica strain CCMP531 ZnCys-2845 orthologs is provided as SEQ ID NO:22. The N. oceanica ZnCys-2845 ortholog PAS3 domain (SEQ ID NO:22) is 86% identical in sequence to the N. gaditana PAS3 domain (SEQ ID NO:21). The PAS3 domain of the N. salina strain CCMP537 ZnCys-2845 ortholog is provided as SEQ ID NO:23, which is 98% identical to the N. gaditana ZnCys-2845 PAS3 domain (SEQ ID NO:21). The PAS3 domain of the N. oculata strain CCMP539 ZnCys-2845 ortholog is provided as SEQ ID NO:24, and it demonstrates 86% sequence identity to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21). As provided above, the PAS3 domain of the ZnCys-2845 ortholog of N. granulata strain CCMP529 is provided as SEQ ID NO:22, which is approximately 86% identical to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

An alignment of the amino acid sequence encoded by the N. gaditana ZnCys-2845 gene and the amino acid sequence (SEQ ID NO: 17) encoded by the N. oceanica strain WT-5473 ortholog of the ZnCys-2845 gene, both of which were determined by in-house genome sequencing and gene assignment, is provided in FIG. 10. Genome sequences of three additional Nannochloropsis species, N. granulata strain CCMP529, N. oculata strain CCMP539, and N. salina strain CCMP537, were further examined to attempt to stitch together protein-encoding sequences of putative ZnCys-28545 orthologs as characterized by the PAS3 domains. The six Nannochloropsis genomes were curated to find regions of homology extending outward from the PAS3 domains. Blastn was utilized to identify homologous sequences, which were linked together with gaps introduced to maximize homology.

The Zn(2)-Cys(6) domain of N. oceanica is identical to the Zn(2)-Cys(6) domain of N. gaditana (SEQ ID NO:3). The polypeptides encoded by the two genes (N. gaditana ZnCys-2845 and the N. oceanica ortholog) have 56% identity across the entire deduced polypeptide sequence, and 71% identity across the first 517 amino acids of N. gaditana ZnCys-2845 (SEQ ID NO:2), a portion of the amino acid sequence that extends from the N-terminus of the protein through the Zn(2)-Cys(6) domain and through the PAS3 domain (see FIG. 5). Amino acids 1-200 encoded by the N. salina ZnCys-2845 homologous sequence (SEQ ID NO:20) have approximately 98% identity to corresponding amino acid sequence of N. gaditana ZnCys-2845 (SEQ ID NO:2); whereas the incomplete polypeptide sequence of a putative ortholog of N. granulata (SEQ ID NO: 18) is approximately 61% identical to N. gaditana ZnCys-2845 (SEQ ID NO:2) and the incomplete polypeptide sequence of a putative ortholog of N. oculata (SEQ ID NO: 19) is approximately 61% identical to N. gaditana ZnCys-2845 (SEQ ID NO:2). These partial polypeptide sequences do not include the PAS3 domains of the Nannochloropsis orthologs, which, as noted above, have much higher % identities to the PAS3 domain of N. gaditana ZnCys-2845 (SEQ ID NO:21).

Example 6 Growth and Lipid Biosynthesis of ZnCys-2845 Knockout Mutant in Semi-Continuous Production System Using Urea Nitrogen Source

To determine whether the ZnCys-2845 gene disruption knockout mutant could utilize other sources of nitrogen, a semi-continuous productivity assay was set up in which the culture medium included urea as the sole nitrogen source.

For assays in cultures that included urea as the sole nitrogen source, seed cultures (also referred to as “starter cultures” or “scale-up cultures”) of ZnCys-2845 knockout strain GE-8564 and wild type strain WT-3730 were grown in PM125 medium that included 7.5 mM urea as the sole nitrogen source. For assays in which wild type cells were cultured in nitrate-only medium (PM074), the wild type cells were scaled up in cultures that included the PM074 nitrate-only medium. The GE-8564 ZnCys-2845 knockout mutants were scaled up in cultures that included the PM124 medium that included both nitrate (8.8 mM) and ammonium (5 mM) for the semi-continuous assays that included only nitrate as the nitrogen source in the assay culture medium.

The scale-up cultures were used to inoculate 225 cm² rectangular tissue culture flasks, each of which contained a final total volume of 550 ml of culture after inoculation. The cultures were inoculated so that each 550 ml culture had an initial OD₇₃₀ of 0.9. A typical inoculum volume was approximately 200 ml of scale-up culture that was added to approximately 350 ml of assay culture medium, which was either PM074 (nitrate-only medium) or PM125 (urea-only medium). Cultures were diluted daily at mid-day, when the light intensity was at its peak, by removing 30% of the volume (165 mls) and replacing it with the same volume of the assay medium (either PM074 or PM125) plus an additional 10 ml of deionized water to make up for evaporation (included in the make-up medium). Semi-continuous assays were typically run for 10-14 days. Daily lipid and biomass productivities were only calculated for cultures that had reached steady state (where the increase in growth was equal to the dilution factor for the assay).

Three cultures were initiated per strain. The flasks included stir bars and had stoppers having inserted tubing connected with syringe filters for delivering CO₂ enriched air (1% CO₂, flow rate, 300 ml per min) that was bubbled through the cultures. The flasks were set in a water bath programmed to maintain a constant temperature of 25° C. on stir plates set to 575 rpm during the assay period. Culture flasks were masked with an opaque white plastic to provide a 31.5 cm² rectangular opening for irradiance to reach the culture. The flasks were aligned with the width (narrowest dimension) against an LED light bank that was programmed with a light/dark cycle and light profile that increased until “solar noon” and then declined to the end of the light period. The light profile was designed to mimic a spring day in Southern California: 14 h light: 10 h dark, with the light peaking at approximately 2000 μE (FIG. 6B). The flasks included stir bars and had stoppers with inserted tubing connected with syringe filters for delivering CO₂ enriched air (1% CO₂, flow rate, 300 ml per min). The flasks were set in a water bath programmed to maintain a constant temperature of 25° C. on stir plates set to 575 rpm during the assay period.

Cultures were diluted daily at mid-day, when the light intensity was at its peak by removing 30% of the volume (165 ml) and replacing it with the same volume of the assay medium plus an additional 10 ml of deionized water to make up for evaporation. A 30% dilution rate was empirically determined as the most productive dilution rate for Nannochloropsis, as 50, 30, and 15% daily dilutions resulted in average TOC productivities of 6.5, 9 and 8 g/m²/day, respectively. Semi-continuous assays were typically run for 7-14 days. Daily lipid (FAME) and biomass (TOC) productivities were calculated from cultures that had reached steady state standing crop TOC and FAME density. Volumetric FAME and TOC productivities in (mg/L/day) were calculated by multiplying the volumetric FAME and TOC amounts by the 30% dilution rate. Aerial productivities (g/m2/day) were calculated by dividing the total productivity of the culture by the size of the aperture through which irradiance was permitted:

${\frac{\left( {{volumetric}\mspace{14mu}{productivity}} \right)\mspace{14mu}{mg}}{L*{day}}*\frac{0.55\mspace{14mu} L}{0.00315\mspace{14mu} m^{2}}*\frac{g}{1000\mspace{14mu}{mg}}} = \frac{g}{m^{2}*{day}}$

FIG. 11A shows that the ZnCys-2845 knockout mutant GE-8564, when cultured in the semi-continuous assay where nitrate is the sole source of nitrogen (diamonds), showed a large induction of lipid production at the outset of the assay which subsequently declined steeply after day 3 of the assay such that lipid production fell below that of the non-induced wild type culture by day 10 of the assay, after which it declined to even lower levels. This pattern is consistent with the results of the batch assay of Example 4 which indicated the ZnCys-2845 knockout mutant GE-8564 is induced for lipid production in nitrate-only media.

In contrast, the cultures of the GE-8564 mutant having a disrupted ZnCys-2845 gene cultured in urea-only medium (FIG. 11A, circles) had consistently higher daily FAME productivity than the wild type strain cultured in either nitrate only medium (triangles) or urea-only medium (squares), both of which are conditions in which the wild type strain is not induced for lipid production (as evidenced by the FAME/TOC ratios of these cultures throughout the assay, see FIG. 11C and Table 14, below). Table 11 provides the daily amounts of FAME produced on an areal basis by all strains in the semi-continuous assay along with the percentage increase of the amount of FAME produced by the knockout mutant GE-8564 strain over wild type FAME levels when both were cultured in urea-only culture medium also provided. Average areal FAME productivity for each strain, expressed as g/m²/day, is provided in Table 12. The increase in FAME productivity of the knockout mutant strain GE-8564 over the wild type strain averaged 58% over the course of the thirteen-day assay when both strains were cultured in urea-only medium. It can also be seen that wild type cells cultured in urea-only medium showed, on average, 16% less FAME productivity than wild type cells in nitrate-only medium. The GE-8564 knockout mutant in nitrate-only medium showed increased FAME production with respect to wild type in the first 8 days of the assay and then experienced declines in daily FAME production as the assay progressed, consistent with a nitrogen depletion response.

TABLE 11 FAME (g/m²/day) Produced by ZnCys Knockout and Wild type Strains Cultured with Nitrate or Urea as Nitrogen Source in Semi-Continuous Assay ZnCys-KO ZnCys-KO ZnCys-KO/ % difference ZnCys-KO/ % increase DAY WT/NO3 NO3 NO3 WT/UREA UREA UREA  1 2.48 5.46 120% 1.84 2.64 43%  2 2.41 5.86 143% 2.24 2.70 20%  3 2.45 6.68 172% 2.18 3.08 41%  4 2.23 6.40 187% 2.00 2.80 40%  5 2.45 5.41 121% 1.98 3.05 54%  6 2.40 4.72  97% 2.12 3.57 69%  7 2.46 3.85  57% 1.90 3.55 87%  8 2.47 3.18  28% 2.11 3.46 64%  9 2.54 2.43  −5% 2.07 3.39 64% 10 2.38 1.77 −26% 1.90 3.16 66% 11 2.25 1.27 −43% 1.74 3.25 87% 12 2.35 0.90 −62% 1.89 3.09 63% 13 2.09 0.69 −67% 1.90 3.05 60% Avg. 2.38 3.74  57% 1.99 3.14 57%

Table 12 provides the average daily FAME productivities of the cultures over the thirteen day semi-continuous culture. The average daily FAME productivity for the ZnCys knockout GE-8564 grown in a urea-only medium was 32% higher than the average daily FAME productivity of the wild type strain (WT-3730) grown in nitrate medium (rightmost column). The high FAME productivity value of the ZnCys-2435 knockout in nitrate-only medium is due to the very high FAME production in the first 7 days of the culture. The daily FAME productivity is already declining by day 5 of the culture however, after which it declines well below wild type cultured in nitrate-only medium (FIG. 11A).

TABLE 12 Average Daily FAME Productivity of Semi-Continuous Cultures in Urea-Only or Nitrate-Only Media g/m²/day Avg change Strain FAME v. WT (NO₃) WT-3730 2.38  0% (NO3) WT-3730 1.99 −16% (Urea) ZnCys-KO GE-8564 3.14 32% (Urea) ZnCys-KO GE-8564 3.74 57% (NO3)

FIG. 11B shows that the ZnCys-2845 knockout mutant (GE-8564) cultured in the semi-continuous assay in a nitrate-only medium (diamonds) demonstrated a precipitous drop in biomass production over the course of the assay, declining to levels that were only a fraction of the biomass produced by wild type cells cultured in nitrate medium by the end of the assay. In contrast, during this semi-continuous productivity assay, there was little decline in biomass (TOC) productivity in the ZnCys-2845 gene disruption mutant cultured in urea medium (circles) with respect to the wild type strain cultured in nitrate medium (triangles), and the ZnCys-2845 knockout mutant even demonstrated slightly better productivity than wild type cultured in urea medium (squares), all three of which remained in fairly consistent over the entire course of the assay.

Table 13 provides the TOC content of these semi-continuous cultures and the percentage difference in the daily amount of TOC produced between the ZnCys-2845 knockout mutant cultured in nitrate-only medium with respect to wild type cells cultured in nitrate-only medium, and the percentage difference in daily TOC produced between the ZnCys-2845 knockout mutant cultured in urea medium with respect to wild type cells cultured in urea medium. In Table 13 the reduction in the amount of biomass produced on a daily basis can be seen in ZnCys-2845 knockout mutant cultured in nitrate only medium as the assay progresses. The biomass production levels of the other cultures, including the ZnCys-2845 knockout mutant cultured in urea medium that had a 58% increase in daily FAME productivity with respect to wild type in urea medium, remains quite consistent throughout the thirteen day assay, and has a slightly better average TOC productivity than does the wild type strain cultured in urea medium. Thus, the ZnCys-2845 knockout mutant was able to accumulate biomass at levels at least equivalent to the wild type strain while demonstrating nearly 60% higher daily FAME productivity when cultured in a medium that included urea as the sole source of nitrogen.

TABLE 13 Biomass (g/m²/day TOC) Produced by Strains Grown in Nitrate or Urea in a Semi-Continuous Assay ZnCys-KO ZnCys-KO ZnCys-KO/ % difference WT/ ZnCys-KO/ % increase, WT/NO3 NO3 NO3 UREA UREA UREA DAY medium medium medium medium medium medium  1 9.65 11.00   14% 8.06 8.86 10%  2 9.24 9.69    5% 7.94 8.25  4%  3 9.42 9.61    2% 8.35 8.80  5%  4 10.28 8.72 −15% 9.21 8.86 −4%  5 10.08 7.19 −29% 8.85 8.88  0%  6 9.97 6.18 −38% 8.72 9.09  4%  7 9.99 5.07 −49% 8.79 9.29  6%  8 9.42 3.83 −59% 8.03 8.55  6%  9 9.34 3.22 −66% 7.99 8.84 11% 10 9.12 2.46 −73% 7.94 8.57  8% 11 9.32 2.00 −79% 7.74 8.74 13% 12 9.53 1.77 −81% 8.11 8.59  6% 13 9.57 1.45 −85% 8.28 9.25 12% Avg 9.61 5.55 −42% 8.31 8.81  6%

In fact, despite the increased lipid production by the ZnCys-2845 knockout mutant in urea-only medium with respect to wild type cells in nutrient replete (nitrate-only) medium (FIG. 11A and Table 11) the average amount of TOC produced throughout the course of the assay by the ZnCys knockout mutant in urea-containing medium was at least 90% that of wild type cells cultured in nitrate medium, i.e., only about 10% less than that of nitrogen replete wild type cells.

FIG. 11C shows the daily FAME to TOC ratios of the cultures in the semi-continuous assay. These ratios stay fairly consistent for all samples with the exception of the ZnCys-2845 gene disruption mutant (“ZnCys-KO”) cultured in nitrate-only medium (diamonds), which shows FAME to TOC ratios climbing from the first day of culturing up to day 8, after which the ratio begins to decline. These FAME:TOC ratios of the ZnCys-2845 gene disruption mutant cultured in nitrate-only medium are far higher than the FAME:TOC ratios of wild type cultured in both nitrate-only and urea-only medium and the ZnCys-2845 knockout mutant cultured in urea-only medium and are indicative of the classic lipid induction response to nitrogen depletion. FAME to TOC ratios of the mutant and wild type semicontinuous assay cultures are provided in Table 14.

TABLE 14 FAME/TOC Ratios of Cultures Cultured in Nitrate or Urea WT/ ZnCys-KO/ WT/ ZnCys-KO/ DAY NO3 NO3 UREA UREA 1 0.3 0.5 0.2 0.3 2 0.3 0.6 0.3 0.3 3 0.3 0.7 0.3 0.3 4 0.2 0.7 0.2 0.3 5 0.2 0.8 0.2 0.3 6 0.2 0.8 0.2 0.4 7 0.2 0.8 0.2 0.4 8 0.3 0.8 0.3 0.4 9 0.3 0.8 0.3 0.4 10 0.3 0.7 0.3 0.4 11 0.2 0.6 0.2 0.4 12 0.2 0.5 0.2 0.4 13 0.2 0.5 0.2 0.3

The ZnCys-2845 gene disruption mutant cultured in urea-only shows consistently higher FAME:TOC ratios with respect to wild type cells cultured in either nitrate-only or urea only medium, but the FAME:TOC ratio is fairly stable throughout the culture period, in the range of 0.3 to less than 0.5, representing an increase of on average about 45% over wild type. Thus, when urea was used as the sole source of reduced nitrogen in the assay, the ZnCys-2845 gene disruption mutant demonstrated significantly increased partitioning of carbon to lipid (Table 14, FIG. 11C) without a substantial loss of overall carbon assimilation (Table 13, FIG. 11B), resulting in an approximately 57% increase in FAME produced on a daily basis and only an approximately 6% decrease in TOC produced with respect to wild type cells cultured under the same (urea-only) conditions over the course of the assay.

Example 7 CAS9 ZnCys-2845 Knockdown Constructs

Since the ZnCys-2845 knockout line exhibited a significant deficit in TOC productivity concomitant with increased carbon partitioning to lipid in batch growth (Example 4, FIG. 7B), we next investigated whether varying the degree of attenuation of ZnCys-2845 expression would result in engineered strains in which lipid and TOC productivity were better optimized. Additional mutant strains were engineered to have decreased expression of the ZnCys-2845 gene using Cas9/CRISPR genome engineering. Twelve chimeric guide RNAs were designed to target sequences upstream of the ATG, within an intron of the gene, in the 3′ end of the gene but still within the coding sequence, or in the 3′ untranslated region of the gene (FIG. 12A). These constructs described here as “Bash Knockdown constructs” or simply “Bash constructs” because they are designed to insert the donor fragment into a site in a region of the gene where the insertion is expected to allow the targeted gene to be expressed at a lower level than in wild type. (Correspondingly, the strains that include such insertions are referred to as “Bash strains”, “Bashers”, or “Bash Knockdown mutants”.) The twelve 18-nucleotide sequences having homology to the ZnCys-2845 gene (target site sequences) are provided in Table 15.

TABLE 15 Target and Chimeric Guide Sequences for Attenuating ZnCys-2845 Expression “Bash” Gene Attenuation Target Gene Region Target Sequence Site Targeted (18 nt) −1 5′ UTR SEQ ID NO: 51 1 5′ UTR SEQ ID NO: 52 2 5′ UTR SEQ ID NO: 53 3 5′ UTR SEQ ID NO: 54 4 5′ UTR SEQ ID NO: 55 6 Intron in SEQ ID NO: 56 PAS3 domain sequence 7 Intron in SEQ ID NO: 57 PAS3 domain sequence 8 C-terminus SEQ ID NO: 58 9 C-terminus SEQ ID NO: 59 10 C-terminus SEQ ID NO: 60 11 3′ UTR SEQ ID NO: 61 12 3′ UTR SEQ ID NO: 62

Chimeric guide DNA constructs were synthesized as two complementary strands that were annealed to produce a double-stranded construct with a T7 promoter positioned upstream of the guide sequence (that included the 18-nucleotide target sequence in addition to the tracr sequence), and used to produce the chimeric guide RNAs by in vitro transcription and purified as described in Example 3. SEQ ID NO:42 is an example of a generic “sense” strand for producing a guide RNA and SEQ ID NO:43 is an example of a generic “complementary” strand that would be annealed to the sense strand (where the target sequence is again represented by 18 Ns,) for producing the guide RNA by in vitro transcription.

In the present experiments, each chimeric guide RNA was individually transformed into Nannochloropsis Editor strain GE-6791 along with the donor fragment that included a Hyg resistance (“HygR”) cassette (FIG. 4A, SEQ ID NO:44) as described in Example 3. Hygromycin resistant colonies were selected and screened by colony PCR as described using primers adjacent to the targeted regions of the ZnCys-2845 gene. Primers MA-ZnCys-FP (SEQ ID NO:49) and MA-ZnCys-RP (SEQ ID NO:50) were used to confirm the knockout (GE-8564) and donor fragment insertion into introns; primers MA-5′Bash-ZnCys-FP (SEQ ID NO:63) and MA-5′Bash-ZnCys-RP (SEQ ID NO:64) were used to confirm the insertion of the donor fragment into the 5′ regions of the ZnCys-2845 gene; and primers MA-3′Bash-ZnCys-FP (SEQ ID NO:65) and MA-3′Bash-ZnCys-RP (SEQ ID NO:66) were used to confirm the insertion of the donor fragment into the 3′ regions of the ZNCys-2845 gene. Eleven of the twelve guide RNAs resulted in isolates that by colony PCR appeared to have the Hyg gene inserted at the targeted locus (insertion into 5′ UTR target site-1 was not observed.)

Quantitative reverse transcription-PCR (qRT-PCR) was performed on RNA isolated from the knockdown lines to determine whether expression of the ZnCys-2845 gene was in fact reduced in these lines. The ZnCys-2845 Bash Knockdown strains were grown under standard nitrogen replete conditions (PM074 (nitrate-only) medium) and harvested during early stationary phase. Total RNA was isolated from ZnCys-2845 Bash Knockdown cells, using methods provided in Example 1, above. RNA was converted to cDNA BioRad's iScript™ Reverse Transcription Supermix kit according to the manufacturer's protocol. For PCR, Ssofast EvaGreen Supermix (Bio-Rad, Hercules, Calif.) was used along with gene-specific primers. The PCR reaction was carried out on C1000 Thermal Cycler coupled with a CFX Real-time System (BioRad). Primer and cDNA concentrations were according to the manufacturer's recommendation. Primers for amplifying a sequence of the ZnCys-2845 transcript were SEQ ID NO:67 and SEQ ID NO:68. Transcript levels for each sample were normalized against a housekeeping gene with consistent expression levels under different culture conditions (1T5001704; SEQ ID NO:69) and relative expression levels were calculated using the ddCT method using BioRad's CFX Manager software.

FIG. 12B shows that several of the strains had reduced levels of ZnCys-2845 transcript. Of these, strains GE-13108 (ZnCys-2845 Bash-2) and GE-13109 (ZnCys-2845 Bash-3), targeting the 5′ end of the ZnCys-2845 gene, and strain GE-13112 (ZnCys-2845 Bash-12), targeting the 3′ end of the ZnCys-2845 gene, were selected for productivity assays.

Example 8 RNAi Knockdown Construct

In another strategy to determine whether decreasing expression of the ZnCys-2845 gene would allow the cells to accumulate more carbon than the Cas9 knockout while still producing increased amounts of lipid with respect to wild type, an interfering RNA (RNAi) construct was designed for expression in Nannochloropsis cells. The construct included a sequence designed to form a hairpin that included a sequence homologous to a region of the ZnCys-2845 gene (SEQ ID NO:70), followed by a loop sequence and then followed by the inverse sequence to the ZnCys-2845 gene-homologous sequence, driven by the N. gaditana EIF3 promoter (SEQ ID NO:46) and followed by N. gaditana “terminator 9” (SEQ ID NO:71). The construct also included a gene encoding GFP codon optimized for Nannochloropsis (SEQ ID NO:36) under the control of the Nannochloropsis 4AIII promoter (SEQ ID NO:37) and followed by “terminator 5” (SEQ ID NO:38), as well as a gene conferring hygromycin resistance (SEQ ID NO:45) driven by the TCTP promoter (SEQ ID NO:34) and terminated by the EIF3 terminator (SEQ ID NO:35). The construct was linearized and transformed into wild type Nannochloropsis gaditana WT-3730 by electroporation as described.

Hygromycin resistant colonies were screened for the presence of the RNAi construct and positive strains were further screened by qRT-PCR as described in Example 7 for knockdown of the ZnCys-2845 transcript levels.

Example 9 Knockdown Constructs in Batch Assay

ZnCys-2845 RNAi strain GE-13103 and ZnCys-2845 knockdown “basher” strains GE-13108, GE-13109, and GE-13112 were tested in the batch productivity assay described in Example 4 by scaling up the cultures in culture medium PM124 (which includes both NH₄ and NO₃ as nitrogen sources) and by carrying out the assay in PM123 culture medium that includes nitrate as the sole nitrogen source. The ZnCys-2845 Knockout strain GE-8564 and the wild type background strain were run in the same assay as controls.

The results, provided in Tables 16-18 and shown in FIGS. 13A-13C, were startling. All gene attenuation mutants, including original knockout mutant GE-8564 (triangles), produced FAME in amounts greater than wild type (circles) when cultured with nitrate as the sole nitrogen source on all days sampled (FIG. 13A, data provided in Table 16). However, while the original knockout strain GE-8564 (triangles) had a significantly reduced rate of total organic carbon accumulation with respect to wild type (FIG. 13B), in these conditions, the attenuated knockdown strains—the “bash” strains and RNAi strain having reduced expression of the ZnCys-2845 gene—had rates of TOC accumulation close to or (for example in the case of GE-13112 (represented as Xs)) essentially identical to, wild type (FIG. 13B, data provided in Table 17). Remarkably, these ZnCys-2845 knockdown mutants demonstrated FAME to TOC ratios that were significantly enhanced with respect to wild type (FIG. 13C and Table 18), although not as high as the FAME to TOC ratios of the ZnCys-2845 knockout mutant GE-8564, i.e., the carbon partitioning to lipid in these knockdown attenuation strains was intermediate between that of wild type and the ZnCys-2845 knockout strain.

TABLE 16 FAME Productivity of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO₃-Containing Culture Medium (mg/L Culture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day WT % incr % incr % incr % incr % incr 3 159.22 279.72 75.68 260.14 233.36 233.36 40.64 233.36 46.56 242.05 52.02 5 191.33 446.40 133.31 377.8 368.41 368.41 55.98 368.41 92.55 360.89 88.67 7 270.37 599.06 121.57 431.41 460.69 460.69 27.96 460.69 70.39 473.53 75.14

TABLE 17 TOC Productivity of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO₃-Containing Culture Medium (mg/L Culture) BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day WT % diff % diff % diff % diff % diff 3 642.4 608.1 −5.34 615.05 −4.26 627.2 −2.37 497.4 −22.57 281.5 −56.18 5 920.75 827.9 −10.09 836.9 −9.11 913.95 −0.74 713.4 −22.52 408.8 −55.01 7 1188 1044.5 −12.08 1044 −12.12 1175.5 −1.05 929.2 −21.78 558.15 −53.18

TABLE 18 FAME/TOC Ratios of ZnCys-2845 Knockdown Strains Compared to Wild Type in Batch Assay with NO₃-Containing Culture Medium BASH-2 BASH-3 BASH-12 RNAi-7 ZnCys-KO WT 3730 (GE-13108) (GE-13109) (GE-13112) (GE-13103) (GE-8564) Day s.d. s.d. s.d. s.d. s.d. s.d. 3 0.2478 0.0092 0.4599 0.0090 0.4229 0.0096 0.3570 0.0043 0.4690 0.0146 0.8608 0.0334 5 0.2078 0.0012 0.5391 0.0059 0.4514 0.0025 0.3263 0.0106 0.5161 0.0230 0.8824 0.0393 7 0.2276 0.0012 0.5735 0.0051 0.4132 0.0036 0.2942 0.0033 0.4959 0.0069 0.8491 0.0593

FIG. 14A provides a diagram of the ZnCys-2845 gene and FIG. 14B provides a graph showing normalized ZnCys-2845 RNA levels in cultured strains having insertional BASH mutations (“basher” strains GE-13109 and GE-13112), the RNAi construct (ZnCys-2845 RNAi strain GE-13103), or the knockout (KO) mutation (ZnCys-2845 knockout mutant GE-8564) as quantitated by PCR using the methods provided in Example 7. The ZnCys BASH-3 strain GE-13109 demonstrated an approximately 20% reduction in ZnCys-2845 transcript level, the ZnCys BASH-12 strain GE-13112 demonstrated an approximately 50% reduction in ZnCys-2845 transcript level, and the ZnCys-2845 RNAi isolate (GE-13103) demonstrated an approximately 70% reduction in ZnCys-2845 transcript level. FIG. 14C provides a graph of the FAME/TOC ratio and TOC productivity of each strain based on a batch assay in nitrate-only medium as described above, except that in the assay of FIG. 14C, the ZnCys-2845 knockout strain GE-8564) was not precultured in the presence of ammonium but in nitrate-only medium. As summarized in FIG. 14C, in batch growth with no nitrate, all three ZnCys-2845 gene attenuation lines exhibited increases in carbon partitioning to lipid evident at FAME/TOC ratios (see also Table 18) that were intermediate between wild type and ZnCys knockout (strain GE-8564) FAME/TOC ratios. TOC accumulation in the knockdown mutants were nearly equivalent to wild type (the ZnCys RNAi-7 strain GE-13103 having the greatest impairment of only about 20%), showing a substantial improvement over the reduction shown in the ZnCys-2845 knockout mutant which demonstrates an approximately 85% reduction in average daily TOC productivity (FIG. 14C). The daily FAME and TOC values of the batch assay from which the data of FIG. 14C is derived are provided in the graphs of FIGS. 15A and 15B.

Example 10 ZnCys-2845 Knockdown Mutants in the Semi-Continuous Productivity Assay

ZnCys-2845 RNAi strain GE-13103, BASH2 strain GE-13108, BASH3 strain GE-13109, and BASH12 strain GE-13112 were then assayed in the semi-continuous productivity assay described in Example 6, except that in this case the assay medium, PM074, included nitrate as the sole nitrogen source and the knockdown strains were pre-cultured in PM124 medium that included 5 mM ammonium in addition to 8.8 mM nitrate. For the GE-13103 ZnCys-2845 RNAi strain, productivity was assayed in two ways: a first set of semi-continuous assay cultures was inoculated using starter cultures that included the PM074 nitrate-only culture medium, and a second set of GE-13103 semi-continuous assay cultures was inoculated using starter cultures that included 5 mM ammonium in addition to 8.8 mM nitrate (PM124 medium).

The starter cultures were used to inoculate 225 cm² rectangular tissue culture flasks, each of which contained a final total volume of 550 ml of culture after inoculation. The cultures were inoculated so that each 550 ml culture had an initial OD₇₃₀ of 0.9. A typical inoculum volume was approximately 200 ml of scale-up culture that was added to approximately 350 ml of assay culture medium, which was PM074 (nitrate-only medium). Cultures were diluted daily at mid-day, when the light intensity was at its peak, by removing 30% of the volume (165 mls) and replacing it with the same volume of the assay medium (PM074) plus an additional 10 ml of deionized water to make up for evaporation (included in the make-up medium). Thus, assay cultures inoculated from scale-up ZnCys-2845 RNAi cultures that included 5 mM ammonium in the culture medium (PM124 medium) started out with a significant amount of ammonium (e.g., about 2 mM ammonium or less) that progressively declined and was diluted out further during the course of the assay. Semi-continuous assays were typically run for 10-14 days. Daily lipid and biomass productivities were only calculated for cultures that had reached steady state (where the increase in growth was equal to the dilution factor for the assay).

During the course of the semi-continuous assay, daily 30% dilutions were with nitrate-only medium (PM074) for all cultures. In these assays, much more lipid was produced on a daily basis by the GE-13103 RNAi knockdown cells scaled up in nitrate-only medium in the semi-continuous assay (filled-in circles, FIG. 16A) as compared with wild type cells, which were in nitrogen replete conditions (diamonds). The amount of lipid produced on a daily basis by the GE-13103 strain was even higher when the scale-up culture medium included ammonium in addition to nitrate (open circles in FIG. 16A). BASH2 strain GE-13108 (Xs), BASH3 strain GE-13109 (triangles), and BASH12 strain GE-13112 (squares) also produced considerably more FAME in the semi-continuous assay than did the wild type strain.

FIG. 16B provides the daily amount of FAME produced by the knockdown strains in the semi-continuous assay that included nitrate as the sole nitrogen source in the culture medium (PM074 medium). The knockdown strains, which included GE-13108 (5′ Bash2), GE-13109 (5′ Bash3), GE-13112 (3′ Bash12), and GE-13103 (RNAi-7) were pre-cultured in nitrate plus ammonium medium PM124. The RNAi knockdown strain GE-13103 was also assayed after being pre-cultured in nitrate-only medium (PM074), alongside wild type strain WT-3730 pre-cultured in nitrate-only medium (PM074) (which is a nitrogen replete medium for the wild type strain). Knockout strain GE-8564 was cultured separately in nitrate-only (PM074) medium as the culture medium used in the semi-continuous assay. The table of FIG. 16B demonstrates that all of the knockdown strains had higher productivities than the wild type strain when cultured in the semi-continuous assay with regular dilution using a culture medium in which nitrate was substantially the sole nitrogen source (PM074). In this assay, knockdown strain GE-13112 (BASH12), demonstrated production of an average daily amount of FAME that was 83% greater than wild type, and knockdown strain GE-13109 (BASH3), demonstrated production of an average daily amount of FAME that was 81% greater than wild type on nitrate. Knockdown strain GE-13108 (BASH2), demonstrated production of an average daily amount of FAME that was 88% greater than wild type diluted with the same culture medium (PM074) over the course of the assay. Thus, all of the insertional knockdown mutants targeting non-coding regions of the ZnCys-2845 gene demonstrated substantial increases in areal FAME productivity of at least 70% higher (and approximately 80%-90% higher), than wild type cells in nitrate-only culture medium, with only minimal TOC productivity decreases of approximately 5-15% in the GE-13108 (BASH2), GE-13112 (BASH12), and RNAi-7 GE-13103 strains compared to the wild type strain (FIG. 16C). The RNAi-7 strain GE-13103 pre-cultured in nitrate-only medium produced on average is 107% more FAME on a daily basis than wild type cultured under the same conditions. The RNAi-7 strain GE-13103 pre-cultured in a medium that included both ammonium plus nitrate produced on average is 122% more FAME on a daily basis than wild type cultured under the same conditions. Thus, the GE-13103 gene attenuation mutant produced at least twice as much lipid as wild type in a semi-continuous assay in which the cultures were regularly diluted with nitrate-only medium, regardless of the nitrogen source in the pre-culture medium. The knockout mutant, GE-8564, also produced somewhat more FAME than wild type in the assay, although the increase was not as great as for the knockdown mutants (approximately 40% greater than when both were cultured in nitrate-only medium). The amount of FAME produced by knockout mutant GE-8564 cultured in nitrate-only medium fell off drastically beginning at about day 6 of the culture, reflecting large losses in biomass (Table 20).

These improvements in FAME productivity by the knockdown strains are presented as a percentage increase over wild type, averaged over the duration of the culture, in Table 19. All of the knockdown strains (GE-13103, GE-13108, GE-13109, and GE13112) had increases in FAME productivity (i.e., g/m²/day) with respect to wild type over the course of the culture, ranging from 81% to 122% over the course of the entire culture, with even greater productivity increases seen in the first four days of culturing, ranging from 100% (i.e., twice the wild type productivity) to 160%. GE-13103, the RNAi knockdown strain, had the largest productivity increase with respect to wild type over the course of the semi-continuous culture, approximately 100% improvement (when pre-cultured in PM074) and approximately 120% improvement (when pre-cultured in PM124).

TABLE 19 FAME Productivity of Knockdown and Knockout Strains (g/m2/day) Day 1-Day 4 Day 8-Day 11 Day 1-Day 11 Strain s.d. % impr s.d. % impr % impr WT-3730 2.37 0.11 — 2.41 0.08 — 2.43 — GE-13112 (BASH-12) 4.75 0.20 100% 4.14 0.10  72% 4.44  83% GE-13109 (BASH-4) 4.89 0.16 107% 3.90 0.13  62% 4.39  81% GE-13108 (BASH-3) 6.15 0.43 160% 2.84 0.46  18% 4.55  88% GE-13103 (RNAi-7) 5.45 0.17 130% 4.39 0.19  82% 4.95 104% (pre-cultured in NO3) GE-13103 (RNAi-7) 5.83 0.32 146% 4.82 0.26 100% 5.40 122% (pre-cultured in NH4 + NO3) GE-8564 (ZnCys-KO) 2.98 0.20  26% 3.14 0.12  30% 3.22  33% Urea medium GE-8564 (ZnCys-KO) 5.80 0.84 145% 1.16 0.43 −52% 3.39  40% Nitrate medium

The amount of TOC accumulated on a daily basis by the knockdown strains was only slightly to modestly less than the TOC accumulated by wild type in knockdown cultures, GE-13109 (5′ Bash-3), and GE13112 (3′ Bash-12) although it was significantly lower in GE-13108 (5′ Bash-2) and knockout strain GE-8564 cultured in nitrate-only medium (FIG. 16C and Table 20). Nevertheless, the TOC productivity in the RNAi knockdown strain (GE-13103) that exhibited an approximately 100% increase in FAME productivity over 11 days (and approximately 120% increased when precultured with ammonium) was only about 18% reduced with respect to wild type, and the TOC productivities of BASH-12 and BASH-4 knockdown mutant strains GE-13112 and GE-13109 (that demonstrated increases of at least 80% in FAME productivity over eleven days) were decreased by only 5% or less.

TABLE 20 Daily Average TOC Productivity of Knockdown and Knockout Strains Strain g/m²/day s.d. % diff WT 9.50 0.30  0% GE-13112 (BASH-12) 9.43 0.60  −1% GE-13109 (BASH-3) 9.06 0.56  −5% GE-13108 (BASH-2) 6.33 2.32 −33% GE-13103 (RNAi-7) 7.75 0.87 −18% (pre-cultured in NO3) GE-13103 (RNAi-7) 8.27 1.09 −13% (pre-cultured in NH4 + NO3) GE-8564 (ZnCys-KO) 8.86 0.26  −7% Cultured in Urea GE-8564 (ZnCys-KO) 4.68 2.88 −51% Cultured in NO3

The ZnCys-2845 knockdown and knockout cultures all demonstrated increased FAME to TOC ratios as compared to wild type (solid diamonds) in the semicontinuous assay in nitrate medium (FIG. 16D and Table 21). When scaled up in nitrate only medium, the RNAi knockdown strain GE-13103 (closed circles) demonstrated a greater than 100% increase, approximately a 150% increase, in FAME/TOC ratio with respect to wild type and the same GE-13103 strain scaled up in nitrate plus ammonium medium (open circles) demonstrated an 153% increase in their FAME to TOC ratio in the semi-continuous productivity assay (Table 21).

TABLE 21 FAME/TOC Ratios of Knockdown and Knockout Strains Strain fame/toc s.d. % impr WT-3730 0.26 0.02  0% GE-13112 (BASH-12) 0.47 0.01 82% GE-13109 (BASH-3) 0.48 0.02 87% GE-13108 (BASH-2) 0.73 0.05 180%  RNAi-7 0.64 0.02 147%  (precultured in NO3) RNAi-7 0.66 0.04 153%  (precultured in NO3 + NH4) GE-8564 0.36 0.03 41% (ZnCys-KO) Cultured in Urea GE-8564 0.69 0.11 168%  (ZnCys-KO) Cultured in NO3

These genetically engineered knockdown cells were able to partition more of their carbon to lipid than wild type (FIG. 16D). The increased FAME/TOC ratios were particularly notable in the ZnCys RNAi attenuation strain GE13103, as it had only modest reductions in TOC (between about 15% and about 20%, Table 20) coupled with increased FAME with respect to wild type throughout the assay (greater than 100% increase, an approximately 120% increase, Table 19).

Graphs of volumetric FAME and TOC productivities of wild type, Cas9 Editor line GE-6791, and ZnCys-2845 knockdown lines GE-13112 (BASH-12A), GE-13109 (BASH-3A), and GE-13108 (BASH-2A) assayed in a separate semicontinuous assay using nitrate-only medium are provided in FIGS. 17A and 17B (data provided in Table 22 and Table 23), and the average areal (g/m²/day) TOC and FAME productivities of the wild type strain and Cas9 editor line (as controls) and the BASH-3, BASH-12, and RNAi mutants (all pre-cultured in nitrate-only medium) in this assay are summarized in the graph of FIG. 18, where it can be seen that the RNAi strain has the highest FAME productivity of the tested mutants.

TABLE 22 Average Daily FAME Productivity of Knockdown Strains in Semi- Continuous Assay Using Nitrate-only Medium AV DAILY FAME % PRODUCTIVTY INCREASE STRAIN (sd) FROM WT WT 2.42 0 (0.13) ZnCys-BASH-12 4.19 73.1 (0.25) ZnCys-BASH-3 4.48 85.1 (0.35) ZnCys-RNAi-7 4.88 101.7 (0.44) Ng-Cas9+ 2.53 4.5 (0.10)

TABLE 23 Average Daily FAME Productivity of Knockdown Strains in Semi- continuous Assay Using Nitrate-only Medium AV DAILY TOC % PRODUCTIVITY DECREASE STRAIN (sd) FROM WT WT 9.96~(0.47) 0 ZnCys-BASH-12 9.48~(0.42) 4.8 ZnCys-BASH-3 9.04~(0.40) 9.2 ZnCys-RNAi-7 8.09~(0.58) 18.8 Ng-Cas9+ 9.80~(0.45) 1.6

The increases in FAME/TOC were significantly less at the outset of the culture period in the ZnCys RNAi attenuation cultures that had been pre-cultured in a medium containing a mixture of nitrate and ammonium than in the ZnCys RNAi attenuation cultures that had been pre-cultured in a medium containing only nitrate (FIG. 16D). Thus it appeared that strains pre-cultured in nitrate plus ammonium media included reduced nitrogen (ammonium) from the pre-culture that was introduced into the assay cultures, and this residual ammonium repressed lipid biosynthesis to some degree. This effect disappeared by the fifth day of the assay (see FIG. 16A, open circles (RNAi strain precultured with ammonium in the medium) versus solid circles (RNAi strain precultured with only nitrate in the medium)), by which time the rate of production of lipid by the ZnCys RNAi attenuation strain did not significantly differ between cultures that had been inoculated with a seed culture that included ammonium and nitrate and cultures that had been inoculated with a seed culture that included only nitrate as a nitrogen source. At this point presumably the cultures that had been pre-cultured in medium that included ammonium ran out of their reduced nitrogen source and induced lipid biosynthesis to approximately the same degree as the cultures that had not been pre-cultured in an ammonium-containing medium. This interpretation was supported by analysis of the nitrogen present in the cultures. For total nitrogen (TN) analysis of cell pellets, 10 ml culture samples were spun down, the media removed from the pellets, and each pellet was resuspended in 1 ml nanopure H₂O, which was then transferred to a 22 ml vial, to which 19 ml of nanopure H₂O was added. Total nitrogen analysis was performed using a Shimadzu TOC-V_(CSH)/VN_(M-1) analyzer. FIG. 19 shows that the amount of total nitrogen in the cell pellets was significantly higher in the GE-13103 cultures that had been inoculated with a pre-culture that included ammonium in the medium (open circles) than in in the cultures that had been inoculated with a pre-culture that included only nitrate (NO₃) (e.g., closed circles). Thus it appeared that the ZnCys RNAi attenuation cells, while able to utilize nitrate for growth (as evidenced by continued TOC accumulation, e.g., FIG. 16C), still induced lipid biosynthesis as long as ammonium was present at low concentrations, for example, of less than about 2 mM or less than about 1.5 mM.

The relationship between the amount of ammonium present in the ZnCys-2845 RNAi strain GE-13103 cultures during semi-continuous assays was investigated in semi-continuous productivity assays performed as described above in which daily samples were analyzed for nitrogen content of the whole culture (culture medium plus cells) as well as FAME content as described in the examples above.

FIG. 20 shows the amount of FAME and nitrogen present in the culture on successive days of semi-continuous culture graphically. Whole culture total nitrogen (TN) was determined by removing a 2 ml sample of the culture to a 22 ml vial, to which 18 ml of nanopure H₂O was added, and analyzing the sample using a Shimadzu TOC-V_(CSH)/VN_(M-1) analyzer. The amount of nitrate that could be accounted for in the PM074 medium was subtracted from the total nitrogen of the sample to arrive at the amount of nitrogen present as ammonium indicated in FIG. 19. Because the ammonium present in the PM124 starter culture was progressively diluted out of the cultures that were inoculated with PM124 (NH₄+NO₃) starter cultures, it can be seen that for this sample, FAME production (open diamonds) rises as ammonium concentration (solid diamonds) falls. Ammonium levels in the culture below about 2.5 mM, and especially below about 2 mM, appeared to result in induction of FAME production in the attenuated RNAi strain (open diamonds).

Example 11 Relationship of Productivity of ZnCys-2845 Attenuation Mutants to Available NH₄ Concentration

The relationship between nitrogen availability and FAME productivity in the ZnCys-2845 RNAi strain GE-13103 was further investigated in a semi-continuous productivity assay as described in Example 10 except that the semi-continuous assay was performed in three separate culture media in which the concentration of ammonium was held constant at three different levels. Wild type Nannochloropsis gaditana (WT-3730) was also included in the assay, where the wild type strain was cultured in the standard PM074 medium that included no ammonium (but included 8.8 mM nitrate as the sole source of nitrogen).

In this experiment, starter cultures that included culture medium containing either 0.5 mM, 1.0 mM, or 2.5 mM ammonium in addition to 8.8 mM nitrate were used to inoculate assay flasks that included culture media that included the corresponding amount of ammonium (in addition to 8.8 mM nitrate). After reaching steady state the cultures were diluted back daily with the ammonium-supplemented media, such that one set of triplicate cultures in which the assay medium included 0.5 mM ammonium was inoculated from a seed culture that included 0.5 mM ammonium and was diluted daily with a medium containing 0.5 mM ammonium throughout the assay, another set of triplicate cultures was inoculated from a seed culture that included 1.0 mM ammonium and included 1.0 mM throughout the assay, and a third set of triplicate cultures was inoculated from a seed culture that included 2.5 mM ammonium and included 2.5 mM ammonium throughout the assay. In each case, the medium was PM074 that includes 8.8 mM nitrate as the sole source of nitrogen that can be used by the microorganisms, supplemented with the appropriate amount of NH₄Cl as well as with 5 mM Hepes, pH 7.5. The results can be seen in Tables 22-24. All samples were assayed in triplicate, and provided values are the average of the three cultures.

FIG. 21A shows the amount of FAME present in the culture on successive days of semicontinuous culture for cultures held at 0.5 mM, 1.0 mM, and 2.5 mM ammonium (solid diamond and triangles, representing RNAi symbols). It can be clearly seen that reducing the ammonium concentration of the culture from 2.5 mM (squares) to 1.0 mM (triangles) increases FAME productivity, which is increased even further when the ammonium concentration is maintained at 0.5 mM (Xs) (see also Table 24).

TABLE 24 Daily FAME Content (mg/L) of Cultures: Average of Triplicate FAME Values (sd) Strain Day 1 Day 2 Day 3 Day 4 Day 5 Day 6 Day 7 Day 8 Day 9 Day 10 WE-3730 44.3 46.31 48.63 48.27 45.91 44.35 45.73 46.48 45.07 41.15 (0.32) (1.53) (1.87) (0.76) (1.66) (1.47) (0.16) (0.81) (0.91) (5.94) GE-13103 35.9 35.5 39.0 35.3 32.5 29.7 35.1 42.3 57.8 41.2 2.5 mM NH4Cl (2.92) 3.24 0.16 0.46 3.36 4.15 2.01 5.09 0.80 3.17 GE-13103 60.0 58.3 58.8 55.3 51.7 48.2 52.5 57.6 60.9 54.5 1.0 mM NH4Cl (1.85) (1.20) 94.290 (0.79) (5.83) (5.75) (6.97) (1.92) (1.11) (1.41) GE-13103 83.5 85.8 87.4 84.4 81.1 75.4 73.9 78.4 83.6 76.9 0.5 mM NH4Cl (0.86) (0.290 (0.980 (0.550 (5.130 (3.37) (3.80) (3.35) (4.60) (3.11)

The FAME productivity is provided in the table of FIG. 21B. The FAME productivity of the GE13103 knockdown strain in 2.5 mM NH₄ medium is reduced by about 15% with respect to wild type FAME productivity in nitrate-only medium (which does not induce lipid production in the wild type strain). At lower ammonium concentrations however, the knockdown mutant shows greater FAME productivity over the course of the assay than does the wild type strain. For example, in culture medium in which the ammonium concentration is 1 mM, the knockdown mutant strain demonstrates an increased average daily FAME productivity of 22%, while at 0.5 mM ammonium, GE-13103 demonstrates an increased average daily FAME productivity of 77% with respect to the wild type strain, that is, the GE-13103 knockdown strain at very low ammonium concentration produces almost twice as much FAME lipids as wild type.

Nevertheless, FIG. 21C shows that reducing the ammonium concentration of the culture medium below 2.5 mM NH₄ does not have a major effect on TOC accumulation by the GE13103 knockdown mutant (Table 25).

TABLE 25 Daily TOC Content (g/m²/day): Average of Triplicate Values (sd) Strain Day 1 Day 2 Day 3 Day 4 Day 5 Day 6 Day 7 Day 8 Day 9 Day 10 Day 11 WT-3730 179.3 177.35 181.7 181.57 172.43 173.7 172.13 171.67 174.1 185 189.47 (7.56) (3.04) (1.56) (7.38) (6.09) (5.36) (3.50) (4.44) (4.36) (2.19) (4.35) GE-13103 137.7 131.1 132.5 123.2 118.6 125.2 127.9 134.9 143.2 153.0 167.5 2.5 mM NH4 (5.59) (6.92) (1.70) (10.63) (13.35) (13.36) (11.15) (5.61) (4.55) (7.74) (12.62) GE-13103 155.2 155.7 152.2 153.0 147.3 163.2 151.2 155.3 162.8 170.0 176.1 1.0 mM NH4 (10.53) (14.08) (12.84) (15.22) (16.67) (8.20) (19.97) (15.51) (13.06) (11.60) (10.77) GE-13103 164.4 167.7 169.1 166.2 160.2 159.7 155.8 160.2 164.3 169.1 172.4 0.5 mM NH4 (4.95) (4.74) (6.86) (5.11) 7.06) (6.33) (7.68) (5.65) (6.22) (1.99) (7.35)

For example, the average daily TOC productivity of the knockdown mutant strain cultured in 0.5 mM ammonium was essentially identical to that of wild type cultured under nitrogen replete (nitrate only) conditions (FIG. 21D). Thus, the GE-13103 knockdown mutant demonstrated at least 75% more lipid productivity while demonstrating no reduction in biomass productivity with respect to wild type cells in nitrogen replete conditions over a period of at least 10 days of culturing. As shown in FIG. 21F, cell counts, as determined by flow cytometry, remained reasonably consistent for a given ammonium concentration throughout the assay, indicating that the cells were actively dividing throughout the semi-continuous assay under all conditions, including conditions in which the low-ammonium cultures were induced for lipid biosynthesis, as indicated by the elevated FAME/TOC ratios of the 1 mM ammonium and 0.5 mM ammonium-containing cultures (as demonstrated in FIG. 21E).

The FAME to TOC ratio of the GE-13103 knockdown mutant cultured in medium having varying ammonium concentrations is shown in FIG. 21E. The FAME to TOC ratio remains between about 0.3 and 0.4 when the ammonium concentration is between about 1 mM and about 2.5 mM, but increases further when the ammonium concentration drops from about 1.0 mM to about 0.5 mM, remaining close to 0.5 throughout the assay using 0.5 mM ammonium in the medium, for example well within the range of between about 4.0 and about 6.0, and within the region of between about 4.5 and about 5.5 (see Table 26).

TABLE 26 FAME/TOC Ratios: Average of Triplicate FAME/TOC Values (sd) Strain Day 1 Day 2 Day 3 Day 4 Day 5 Day 6 Day 7 Day 8 Day 9 Day 10 WT-3730 0.2 0.3 0.27 0.27 0.27 0.26 0.27 0.27 0.26 0.22 (0.01) (0.01) (0.01) (0.01) (0.00) (0.00) (0.01) (0.01) (0.00) (0.03) GE-13103 0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.4 0.3 2.5 mM NH4Cl (0.01) (0.01) (0.00) (0.00) (0.01) (0.01) (0.01) (0.03) (0.01) (0.01) GE-13103 0.4 0.4 0.4 0.3 0.4 0.3 0.3 0.4 0.4 0.3 1.0 mM NH4Cl (0.00) (0.00) (0.01) (0.01) (0.00) (0.00) (0.00) (0.03) (0.03) (0.01) GE-13103 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 mM NH4Cl (0.02) (0.01) (0.01) (0.01) (0.01) (0.02) (0.02) (0.00) (0.01) (0.01)

Thus, the strains obtained by attenuating expression of a gene as provided here that regulates lipid biosynthesis are able to actively divide while producing considerably more lipid than wild type. The ability to sustain elevated levels of lipid production without a decline in TOC accumulation throughout the assay (FIGS. 22A-22E), indicates the mutants provided herein can provide sustained high-level lipid production such as in continuous and semi-continuous cultures.

Example 12 Analysis of Protein, Carbohydrate, and Lipid Content of ZnCys Mutants

In the above experiments (e.g., Example 4), FAME and TOC productivities of knockout mutant strain GE-8564 were found to be essentially equal to those of the wild type strain when both were cultured in the presence of ammonium (FIGS. 8A-8C), suggesting that a bottleneck in nitrate assimilation led to the marked phenotypes of increased lipid production that were observed only when nitrate was used as the sole nitrogen source. Knockdown mutants of ZnCys-2845 were observed to exhibit substantial increases in FAME productivity (Table 16 and FIG. 13A as well as FIGS. 16A and 16B) with minimal TOC decreases of from about 1% to about 33% (Table 17 and FIG. 13B; FIG. 16C). FAME and TOC productivities for a semi-continuous assay that included wild-type, ZnCys-2845 BASH-3, ZnCys-2845 BASH-12, and ZnCys-2845 RNAi strain GE-13103 are shown in the graphs of FIGS. 17A and 17B, respectively. ZnCys BASH-3, ZnCys BASH-12, and ZnCys RNAi all exhibited substantial increases in aerial FAME productivity (up to 103% for ZnCys RNAi-7) with only minimal TOC decreases of approximately 5-15% compared to the wild type strain and the Cas9 progenitor line (FIG. 18). To determine how carbon was allocated to major categories of biomolecules, the strains were grown in the semi-continuous assay system as described in Example 10, where the PM074 dilution medium included nitrate as the sole nitrogen source. In this assay the RNAi line demonstrates increased FAME productivity and the knockout line is unable to maintain growth (FIGS. 22A-E). The strains from these cultures were assessed for carbohydrate, lipid, and protein, which together accounted for about 75% of TOC.

For HPLC analysis of lipids, 2 ml samples of each culture were spun down at maximum speed for 5 minutes, the supernatants were removed, and pellets were re-suspended in 400 μL of H₂O. The cell suspensions (approximately 500 μL) were transferred to 4 ml glass vials with Teflon lined caps. 500 μL of glass beads (212-300 m diameter) were added to each of the cell suspensions, after which 50 μL of 50% H₂SO₄ and 100 μL of 5M NaCl were added. Bead beating was performed for 5 minutes at 1 krpm, then 2 ml of hexane was added to each sample, and bead beating was repeated for 5 minutes at 1 krpm. The samples were loaded onto a multi-tube vortexer and shaken for 30 minutes at 1 krpm, and then vortexed for 30 seconds at 2.5 krpm. 500 μL of the organic layer was transferred to an HPLC vial, and 50 μL of internal standard solution (1 mg/ml 6-ketocholestanol in toluene) was added to each vial. Standards were from NuCheck, Sigma-Aldrich, or Supelco. The vials were capped and vortexed briefly (5 seconds at 2.5 krpm) prior to HPLC analysis. The HPLC was run at a flow rate of 2 ml/minute on a Chromegasphere SI-60 150 mm×4.6 mm×10 m column (ES Industries), with a column compartment set at 40° C. The injection volume was 25 μL with a draw and eject speed of 200 μL/minute. Eluent A was hexane and Eluent B was an 80:10:10:1 mixture of hexane, isopropanol, ethyl acetate, and 10% formic acid in isopropanol, run as a gradient program as follows: 2% B at 0.0 min; 2% B at 1.0 min; 35% B at 8.0 min; 98% B at 8.5 min; 98% B at 11.5 min; 2% B at 11.6 min; stop time: 11.6 minutes; 5 minutes post time. The detector was ELSD at 30° C. and 3.5 bar N2, with a gain of 5.

Total carbohydrate analysis was conducted on ˜0.7 mg TOC equivalent of cell culture concentrated to 0.5 ml in phosphate buffered saline (PBS) after three centrifugations followed by washing with PBS. Acid hydrolysis was used to convert carbohydrates to their constituent monomers by the addition of 0.5 ml deionized H₂O and 1 ml 6 N HCl and U-¹³C-glucose and -galactose as internal standards at a final concentration of 50 μg/ml each. Samples were heated at 105° C. for one hour in glass vials with PTFE-lined capped. One hundred μl aliquots of the room temperature cooled, 3,000 g centrifuged (1 min) samples were dried in an EZ-2 Genevac (Stoneridge, N.Y.) and derivatized with MSTFA/TMCS and analyzed by GC-MS according to Ruiz-Matute et al. (2011) J. Chromatogr BAnalyt Technol Biomed Life Sci 879: 1226-1240. Internal ¹³C labeled standards were used to quantify the concentration of the major carbohydrate monomers, glucose and galactose, and estimate the concentration of less abundant sugars (arabinose, rhamnose, xylose, and mannose). These were summed to yield a total saccharide concentration in ug/ml which was converted to the carbon content of total carbohydrates by a multiplication factor of 0.45 (i.e., ˜45% of carbohydrate mass is represented by carbon. This value was divided by the amount of TOC detected in an identical aliquot of concentrated cell culture to estimate the percent of carbon allocated to carbohydrate.

Total amino acid analysis was conducted by derivatization of whole amino acid hydrolysate to propoxycarbonyl propyl esters using a modified method according to the EZ:faast kit from Phenomenex (Torrance, Calif.). Briefly, to 0.5 ml concentrated cells (as described for carbohydrate analysis above) 800 ul of 6 N HCl containing 200 μl/ml thioglycolic acid, 10 ul of 3-mecraptoethanol, and 200 ul of 2 mM norvaline (internal standard) were added and the vortexed sample was incubated at 110° C. for 24 h. Samples cooled to room temperature were centrifuged at 1,500 g for 1 minute and a 50 μl aliquot was transferred to a fresh 2 ml GC vial. Aliquots were derivatized and analyzed by GC-MS according to the EZ-faast manual and (8). This method allowed for the quantification of Ala, Gly, Val, Leu, Ile, Pro, Asp+Asn, Met, Glu+Gln, Phe, Lys, Tyr, and Cys; Trp, Thr, Ser, Arg, and His were excluded. Volumetric concentrations of each detected hydrolyzed amino acid was converted to the carbon content present in that amount. These values were summed to and normalized to TOC as described for total carbohydrates above to give an estimate of carbon allocated to protein.

The results are seen in FIG. 23, where it can be seen that both attenuated ZnCys mutants ZnCys-BASH-12 and ZnCys RNAi had decreases of approximately 45-50% in protein compared to the wild type strain, accompanying an approximately 90-125% increase in lipids in the strains. Consistently, the ZnCys knockout strain were observed to have the highest C:N ratios while ZnCys RNAi displayed more intermediate levels (FIG. 22C), suggesting there may be a threshold C:N value that maximizes lipid productivity. The ZnCys knockout strain appears to be beyond that threshold, partitioning so much carbon into lipid that overall biomass and lipid productivity are negatively affected. In contrast, in this set of gene attenuation mutants, the ZnCys RNAi appears to have the optimal C:N value for lipid productivity in the range of about 10-15.

TABLE 27 Protein, Carbohydrate, and Lipid (FAME) % Composition of Wild Type and ZnCys Knockdown Strains Change Change Change Change from from from from STRAIN Protein wt Carb wt FAME wt Other wt WT 40.2 0 11.2 0 19.6 0 29.1 0 (0.55) (0.50) (0.32) (0.27) ZnCys- 22.5 −44% 12.7 +13% 37.6  +92% 27.2 −6.5% BASH-12 (0.70) (0.12) (2.19) (2.94) ZnCys- 20.1 −50% 12.7 +13% 42.7 +118% 24.9  −14% RNAi-7 (2.43) (0.70) (4.73) (1.59)

BASH-12 strain GE-1112 allocated approximately 38% of its carbon to FAME lipids, and approximately 22% of its carbon to protein, while RNAi strain GE-13103 allocated approximately 43% of its carbon to lipid, and approximately 20% of its carbon to protein. This is distinguished from wild type cells in nitrate-only medium that allocate approximately 20% of carbon to lipid, and approximately 40% of carbon to protein. (In both mutants and wild type cells, approximately 10-15% of carbon is allocated to carbohydrates.) Thus both ZnCys gene attenuation (“knockdown”) mutants increased carbon allocation to lipid by 90-120% (doubling lipid productivity with respect to wild type) largely at the expense of allocation of carbon to protein, which dropped by about 40-50% with respect to the carbon allocation to protein in wild type cells cultured under the same conditions.

Example 13 Transcriptomic Analysis of the ZnCys-2845 Knockout and Knockdown Mutants

The ability of ZnCys-2845 knockout strain GE-8564 to accumulate FAME and TOC at levels essentially identical to wild type cells when the culture medium was supplemented with ammonium (Tables 7-9, FIG. 8), indicated the mutant was impaired in nitrate assimilation. To further investigate nitrogen assimilation in these mutants, steady-state mRNA levels of key N-assimilation genes by qRT-PCR were determined to gain a better understanding of N-deficiency in the mutants under induced (nitrate-only medium) and non-induced (ammonium supplementation) conditions.

A nitrate reductase mutant was engineered using the same Cas9 Editor line described in Example 2. Briefly, a guide RNA was designed having the target sequence of a portion of the coding region of the N. gaditana nitrate reductase gene Naga_100699 g1. The guide RNA (having target sequence SEQ ID NO: 193) was synthesized as disclosed in Example 3, and transformed into the Cas9 editor line along with the donor fragment (SEQ ID NO:44) as described in Example 2. The resulting nitrate reductase knockout strain (NR-KO) served as a control for the inability to assimilate nitrate, as a functional nitrate reductase enzyme is necessary to assimilate nitrogen when nitrate is the sole nitrogen source. Effectively, the NR-KO strain is under nitrogen starvation when cultured in nitrate-only medium.

Steady-state mRNA levels of key N-assimilation genes were assessed by qRT-PCR to gain a better understanding of N-deficiency in the mutants under induced (NO₃ ⁻) and non-induced (NH₄ ⁺) conditions, where the nitrate reductase mutant (NR-KO) created by Cas9-mediated mutagenesis was used as an N-starvation control under growth on NO₃ ⁻. When grown on medium that included ammonium all strains shared similar gene expression profiles for the N-assimilation gene set, consistent with their wild type phenotype with regard to biomass and FAME accumulation when cultured with ammonium-containing medium (FIG. 24, ammonium transcriptional profiles of the ZnCys knockout, the ZnCys RNAi knockdown, wild type, and the NR knockout shown in columns 2-5).

TABLE 28 Primer Sequences for Transcripts Measured by Quantitative Real-Time PCR N. gaditana qRT-PCR sense primer/ Gene Description genome ID qRT-PCR antisense primer NAR1 Formate Nitrite Naga_100100g7 GCCAACCTGCCAGTAAAATTC Transporter (SEQ ID NO: 153) AGAGCGGGATTCTGTTCTTG (SEQ ID NO: 154) Amt2 Ammonium Transporter Naga_100099g15 AGAACGTGGGTAAGATGCAAC (SEQ ID NO: 155) ACCAGCCAAACCAGAGAAG (SEQ ID NO: 156) GS2 Glutamine Synthase Naga_100003g119 GGCATACCTATTCATCCGCTAG (SEQ ID NO: 157) CAAATGACCAAGCACCAACTC (SEQ ID NO: 158) NAR2 Nitrite Transporter Naga_100046g36 GCGAGGCATCTTGTGAATTG (NAR1) (SEQ ID NO: 159) ACGGAGTGTTCAAATCCCAG (SEQ ID NO: 160) GS1 Glutamine Synthase Naga_100056g25 CATGGACTCATTCTCCTACGG (SEQ ID NO: 161) ATCCTCGAAATATCCGCACC (SEQ ID NO: 162) GOGAT1 Glutamate Synthase Naga_101084g2 TGGATGCAAACGAGATGCTAG (SEQ ID NO: 163) AGGAAAGCGGGAATAGTGTG (SEQ ID NO: 164) GDH Glutamate Naga_100063g22 GGGACTCGTTGGAAGGTAAG Dehydrogenase (SEQ ID NO: 165) CATTTCCACAAGTTTCTCCGC (SEQ ID NO: 166) GOGAT2 Glutamate Synthase Naga_100005g23 AAGGGAATGTCTTGGAACCG (plastid) (SEQ ID NO: 167) AGTGGGTAGACAGTGGAGAG (SEQ ID NO: 168) NRT2 Nitrate high affinity Naga_100699g1 AGTGCTATGGAGTTTTGCGG Transporter (SEQ ID NO: 169) TTGGGATTTGGTCAAGGAGAG (SEQ ID NO: 170) NiR Nitrite Reductase Naga_100852g1 GCCGATCCTTTCTTGCAAAC (SEQ ID NO: 171) AGCGTTCAATCAGGTCCAAG (SEQ ID NO: 172) NR Nitrate Reductase Naga_100699g1 GCTATATTGGAGAATCCGGCG (SEQ ID NO: 173) GGGAACGTCAACAGTGATAGTG (SEQ ID NO: 174) Amt1 Ammonium Transporter Naga_100551g3g1 CCTTCGGTGCCTATTTCGG AmtB-like protein (SEQ ID NO: 175) CATGTCGCTGGTATAGGATGC (SEQ ID NO: 176) UreT Urea active transporter- Naga_100311g2 ATGGCAGTAGAAATGGACCC like protein (SEQ ID NO: 177) AGTAAGAGAACGAAAAGGGCG (SEQ ID NO: 178) qRT-PCR Protein of Unknown Naga_100004g25 CTCTCCTATTGCTTTCCCTCG control Function (SEQ ID NO: 179) CTACCAACACCTCTACACTTCC (SEQ ID NO: 180)

However, when grown on nitrate as the sole nitrogen source, NR-KO showed a radically different expression profile from the ZnCys mutant lines (FIG. 24, column 1 compared with columns 6 & 7 showing transcriptional profiles of the ZnCys-2845 knockout and RNAi knockdown mutants). Consistent with previous reports on N-deprived N. gaditana (Radakovitz et al. 2012), a large number of genes involved in N-assimilation were severely upregulated in the NR-KO (shown in red color), including two ammonium transporters (AMT1 and AMT2), a glutamate synthase (GOGAT1), a NO₃ ⁻ transporter (NRT2) and nitrite reductase (NiR). Interestingly, this response was not observed for ZnCys mutants. In fact, gene expression profiles for the ZnCys-2845 knockout and the ZnCys-2845 RNAi knockdown engineered mutants more closely resembled wild type under these conditions, though NiR and NRT2 were significantly down regulated in the ZnCys-2845 knockout with respect to wild type, thus offering a possible explanation to the N-deficiency of the cells (FIG. 22C). Analysis of protein levels by Western blotting showed that nitrate reductase could not be detected in extracts of ZnCys-2845 knockout strain GE-8564, while a signal was detected in ZnCys-2845 RNAi knockdown strain GE-13103 extracts as well as wild-type extracts (FIG. 25). Likewise, a very weak signal was observed for the nitrogen assimilation enzyme glutamine oxoglutarate aminotransferase (GOGAT1) in GE-8564, while it was more apparent for GE-13103.

Protein level changes in the plastid lipid biosynthetic machinery were also assessed using specific peptide antibodies against ACCase and fatty acid synthesis (FAS) pathway components (FIG. 25). For antibody production, two peptides (#1 and #2 in Table 29) were synthesized and injected into rabbits. Terminal cysteines are shown for reference.

TABLE 29 Peptide Sequences Used to Generate Antibodies Detecting Fatty Acid Biosynthesis Enzymes in N. gaditana N. gaditana Gene Description genome ID Peptide #1 Peptide #2 ACCase Acetyl-CoA Naga_100605g1 C-FKFADTPDEESPLR C-AENFKEDPLRRDMR Carboxylase (SEQ ID NO: 181) (SEQ ID NO: 182) HAD 3-Hydroxyacyl Naga_100113g7 C-TANEPQFTGHFPER C-IDGVFRKPVVPGD ACP Dehydrase (SEQ ID NO: 183) (SEQ ID NO: 184) ENR Enoyl-ACP Naga_101053g1 C-PEDVPEAVKTNKRY C-AIGGGEKGKKTFIE Reductase (SEQ ID NO: 185) (SEQ ID NO: 186) KAR β-Ketoacyl-ACP Naga_100037g12 C-VAIKADMSKPEEVE C-SDMTEKLDLDGIKK Reductase (SEQ ID NO: 187) (SEQ ID NO: 188) KAS1 β-Ketoacyl-ACP Naga_100002g173 C-YMRGSKGQIYMKEK C-DAKPYFKDRKSAVR Synthase 1 (SEQ 1D NO: 189) (SEQ 1D NO: 190) KAS3 β-Ketoacyl-ACP NG_scf10: MGKRSTASSTGLAY-C C-PPSIREVTPYKGKY Synthase 3 19284 . . . 18979 (SEQ 1D NO: 191) (SEQ 1D NO: 192)

Compared to wild type, levels of these enzymes were not noticeably higher in ZnCys mutants, and in the case in NR-KO, ACCase and KAR1 were reduced. These data suggest that under N-replete conditions the plastid lipid biosynthetic machinery is already present at a capacity that is capable of at least double the flux to fatty acid given the ˜100% increase in FAME productivity observed in ZnCys-2845 RNAi knockdown strain GE-13103. This conclusion is consistent with transcriptional changes observed for N-deprived Nannochloropsis, where pathways involved in providing carbon precursors to lipid biosynthesis appear to be more differentially expressed than “core” lipid biosynthetic pathways (Radakovitz et al 2012, Carpinelli et al 2014, Li et al 2014).

In order to gain further insight into the mechanisms that allow for ZnCys-2845 attenuated lines to constitutively produce lipid and sustain growth, we analyzed the global transcriptional profiles of ZnCys-2845 RNAi strain GE-13103 during steady-state growth conditions (e.g., FIGS. 17A-17B). Using a 2-fold cut-off and FDR<0.05, 1118 genes were found to be differentially expressed between ZnCys-RNAi-7 and wild type in nitrate-only culture medium. Of these, 790 were up-regulated and 328 down-regulated in the mutant. Analysis of the down-regulated gene set for enriched gene ontology (GO) categories by “molecular function”, “biological process” or “cellular component” revealed that genes involved in photosynthesis and light harvesting were overrepresented in the mutant with respect to the wild type (Table 30).

TABLE 30 Overrepresented Gene Ontology Categories Corresponding to Genes that are Down-Regulated in ZnCys_RNAi-7 # genes Over- FDR # genes in represented adjusted Category Ontology^(†) GO Term DE^(††) category pvalue pvalue^(†††) GO:0009765 BP photosynthesis, light 15 17 4.3E−11 7.4E−08 harvesting GO:0016168 MF chlorophyll binding 15 22 4.3E−08 2.4E−05 GO:0018298 BP protein-chromophore 15 22 4.3E−08 2.4E−05 linkage GO:0009523 CC photosystem II 18 39 1.3E−06 5.7E−04 GO:0003824 MF catalytic activity 98 399 2.6E−05 8.9E−03 ^(†)BP, Biological process; CC, cellular component; MF, molecular function ^(††)DE, Differentially expressed genes ^(†††)FDR, False Discovery Rate

The same analysis conducted on the up-regulated gene set revealed that components of protein synthesis were significantly enriched for in the attenuated ZnCys-2845 RNAi strain GE-13103 (Table 31). Considering that our analysis of biomass composition indicated an approximately 45% decrease in total protein content in GE-13103 (FIG. 23), the up-regulation of translation machinery and down-regulation of photosynthetic apparatus is likely a response to that deficit.

TABLE 31 Overrepresented Gene Ontology (GO) Categories Corresponding to Genes that are Up-Regulated in ZnCys-2845 RNAi Strain GE-13103 # genes Over- FDR # genes in represented adjusted Category Ontology^(†) GO Term DE^(††) category pvalue pvalue^(†††) GO:0006412 BP translation 88 175 1.9E−26 3.1E−23 GO:0005840 CC ribosome 77 160 5.1E−24 4.4E−21 GO:0003735 MF structural constituent 68 138 1.2E−22 6.5E−20 of ribosome GO:0005622 CC intracellular 85 226 1.1E−11 4.6E−09 GO:0005737 CC cytoplasm 70 183 3.4E−07 1.2E−04 GO:0000166 MF nucleotide binding 175 525 5.5E−07 1.4E−04 GO:0005524 MF ATP binding 206 636 5.6E−07 1.4E−04 GO:0005852 CC eukaryotic translation 10 11 2.2E−06 4.6E−04 initiation factor 3 complex GO:0003743 MF translation initiation 26 55 1.5E−05 2.8E−03 factor activity GO:0005694 CC chromosome 12 18 2.3E−05 3.5E−03 GO:0006413 BP translational initiation 26 56 2.3E−05 3.5E−03 GO:0030529 CC Ribonucleo-protein 34 109 2.9E−05 4.1E−03 complex GO:0006260 BP DNA replication 20 37 1.1E−04 1.4E−02 GO:0015935 CC small ribosomal subunit 8 13 2.0E−04 2.4E−02 GO:0005874 CC microtubule 17 30 4.3E−04 4.3E−02 GO:0001731 BP formation of translation 5 5 4.9E−04 4.3E−02 preinitiation complex GO:0006446 BP regulation of 5 5 4.9E−04 4.3E−02 translational initiation GO:0016282 CC eukaryotic 43S 5 5 4.9E−04 4.3E−02 preinitiation complex GO:0033290 CC eukaryotic 48S 5 5 4.9E−04 4.3E−02 preinitiation complex GO:0051082 MF unfolded protein 14 28 5.4E−04 4.4E−02 binding GO:0007155 BP cell adhesion 8 10 5.5E−04 4.4E−02 ^(†)BP, Biological process; CC, cellular component; MF, molecular function ^(††)DE, Differentially expressed genes ^(†††)FDR, False Discovery Rate

Consistent with our qRT-PCR findings (FIG. 24), analysis of N-assimilation genes revealed a few key down-regulated genes that could account for the low N-levels in the mutant, including nitrite reductase, two glutamine synthetases (GS1 and GS2), an ammonium transporter (AMT1) and a key enzyme involved in molybdenum cofactor biosynthesis (MoeA/CNX1), a cofactor that is essential for nitrate reductase activity (Table 29).

TABLE 32 Average Transcript Levels and Fold Changes of Differentially Expressed Genes Involved in N-Assimilation ZnCys WT RNAi-7 FC^(††) Gene Alias N. gaditana id Description (FPKM) ^(†) (FPKM) ^(†) (log₂) FDR^(†††) Amt3 Naga_102173g1 Ammonium transporter 2.3 14.7 2.5 3.8E−06 AmtB-like protein Amt2 Naga_100099g15 Ammonium transporter 635.9 841.4 0.4 5.5E−02 NAR2 Naga_100100g7 Formate nitrite transporter 40.3 42.7 0.1 8.3E−01 UreT Naga_100311g2 Urea active transporter- 6.4 6.5 −0.1 7.9E−01 like protein NAR1 Naga_100046g36 Nitrite transporter 137.1 128.2 −0.1 5.2E−01 GOGAT2 Naga_100005g23 Glutamate synthase 54.1 48.9 −0.2 5.0E−01 (plastid) GOGAT1 Naga_101084g2 Glutamate synthase 8.7 7.2 −0.3 7.3E−01 NR Naga_100699g1 Nitrate reductase 336.1 283.2 −0.3 2.4E−01 NRT2 NG_SCF17:5277-7851 Nitrate high affinity 1650.0 1368.4 −0.3 1.0E−02 transporter GS1 Naga_100056g25 Glutamine synthetase 2084.4 1529.3 −0.5 3.4E−03 GDH1 Naga_100063g22 Glutamate dehydrogenase 317.5 205.4 −0.7 9.7E−06 GS2 Naga_100003g119 Glutamine synthetase 6.5 3.9 −0.7 4.3E−02 NiR Naga_100852g1 Nitrite reductase 783.2 499.2 −0.7 2.3E−04 MoeA/CNX1 Naga_101167g3 Molybdenum cofactor 207.0 83.0 −1.4 6.2E−14 biosynthesis protein Amt1 Naga_100551g3 Ammonium transporter 126.9 16.7 −2.9 7.9E−36 AmtB-like protein ^(†)FPKM, Fragments per kilobase of transcript per million mapped reads ^(††)FC, Fold change of genes in ZnCys-RNAi-7 relative to WT ^(†††)FDR, False Discovery Rate

The GO category analysis did not find a statistical enrichment for genes involved in lipid biosynthesis. However, when the list was manually curated, 26 genes related to glycerolipid biosynthesis were identified as upregulated using the same filtering criterium as above (Table 30). These genes included six fatty acid desaturases, elongases, lipases and acyltransferases of unknown substrate specificity, and the lipid droplet surface protein (LDSP) which is believed to be the main structural component of the lipid droplet (Vieler et al. (2012) Plant Physiol. 158:1562-1569).

TABLE 33 Average Transcript Levels and Fold Changes of Differentially Expressed Genes Involved in Glycerolipid Biosynthesis ZnCys- WT RNAi-7 FC^(††) N. gaditana id Description (FPKM) ^(†) (FPKM) ^(†) (log₂) FDR^(†††) Naga_100092g4 Omega-6 fatty acid desaturase delta-12 1.0 13.8 4.0 1.0E−11 Naga_100004g102 Elongation of fatty acids protein 19.6 120.0 2.6 2.9E−14 (EC 2.3.1.199) Naga_100086g4 Lipid droplet surface protein 280.3 1608.6 2.5 7.4E−34 Naga_100040g9 Acyl transferase/acyl 0.7 2.0 2.2 7.9E−04 hydrolase/lysophospholipase Naga_100042g43 Nadp-dependent glyceraldehyde-3- 14.2 63.0 2.1 5.2E−08 phosphate dehydrogenase Naga_100042g12 Delta 5 fatty acid desaturase 11.3 46.8 2.0 5.0E−11 Naga_100035g27 CDP-diacylglycerol pyrophosphatase 1.0 4.3 2.0 3.2E−06 Naga_100162g4 Elongation of fatty acids protein 7.3 28.5 1.9 5.9E−07 (EC 2.3.1.199) Naga_100257g1 Glyceraldehyde-3-phosphate 20.0 74.9 1.8 2.2E−14 dehydrogenase (EC 1.2.1.12) Naga_100937g1 Acyltransferase 3 (Fragment) 1.6 6.2 1.8 1.9E−04 Naga_100273g7 Delta 5 fatty acid desaturase 12.2 42.2 1.8 2.4E−08 Naga_100001g58 Glyceraldehyde-3-phosphate 25.8 87.8 1.7 4.8E−17 dehydrogenase (EC 1.2.1.12) Naga_100426g5 Lipase, class 3 1.0 4.6 1.7 7.5E−05 Naga_100012g35 Lipase domain-containing protein 0.3 1.6 1.6 2.8E−03 Naga_100226g14 Acyltransferase 3 2.3 6.6 1.6 6.5E−07 Naga_100241g4 Lipase 0.7 2.6 1.4 2.0E−03 Naga_100075g9 Delta(5) fatty acid desaturase B 6.0 16.1 1.4 9.0E−05 Naga_100115g11 Stearoyl-CoA 9-desaturase 23.8 63.1 1.4 4.0E−14 Naga_102092g1 Acyl-CoA Synthase 5.3 13.1 1.3 8.5E−04 Naga_100063g13 Delta 3 fatty acid desaturase 25.6 59.7 1.2 6.0E−09 Naga_100530g1 Lipase-like protein 1.7 3.9 1.1 2.1E−02 Naga_100028g54 Acetyl-coenzyme A synthetase 16.9 36.8 1.1 1.3E−10 (EC 6.2.1.1) Naga_101607g1 Triglyceride lipase-cholesterol esterase 53.7 115.3 1.1 1.9E−06 Naga_100247g4 Patatin-like phospholipase domain- 114.3 54.5 −1.1 2.0E−09 containing protein 2 Naga_100529g6 Lipase, class 3 (Fragment) 291.2 134.6 −1.1 2.1E−13 Naga_100771g2 Acyltransferase 3 14.1 3.6 −2.0 5.4E−15 ^(†)FPKM, Fragments per kilobase of transcript per million mapped reads ^(††)FC, Fold change of genes in ZnCys-RNAi-7 relative to WT ^(†††)FDR, False Discovery Rate (transcript levels are shown for genes with FDR <0.05)

Consistent with our Western blot data for ACCase and FAS (FIG. 25), transcripts encoding these enzymes were not found to be differentially expressed in the mutant with respect to wild type, nor was differential regulation of genes encoding diacylglycerol acyltransferases (DGATs) or other enzymatic steps leading to TAG biosynthesis observed. 

What is claimed is:
 1. A method of producing lipid, comprising culturing a classical mutagenesis derived or genetically engineered mutant algal or heterokont microorganism that produces at least 30% more fatty acid methyl ester-derivatizable lipids (FAME lipids) than a control algal or heterokont microorganism and at least 45% of the amount of biomass produced by the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions under which the control microorganism is producing biomass, wherein the mutant microorganism has attenuated expression of a gene encoding a polypeptide comprising an amino acid sequence having at least 80% identity to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:17.
 2. The method of claim 1, wherein the mutant microorganism is a species of Achnanthes, Amphiprora, Amphora, Ankistrodesmus, Asteromonas, Boekelovia, Bolidomonas, Borodinella, Botrydium, Botryococcus, Bracteococcus, Chaetoceros, Carteria, Chlamydomonas, Chlorococcum, Chlorogonium, Chlorella, Chroomonas, Chrysosphaera, Cricosphaera, Crypthecodinium, Cryptomonas, Cyclotella, Desmodesmus, Dunaliella, Elipsoidon, Emiliania, Eremosphaera, Ernodesmius, Euglena, Eustigmatos, Franceia, Fragilaria, Fragilaropsis, Gloeothamnion, Haematococcus, Hantzschia, Heterosigma, Hymenomonas, Isochrysis, Lepocinclis, Micractinium, Monodus, Monoraphidium, Nannochloris, Nannochloropsis, Navicula, Neochloris, Nephrochloris, Nephroselmis, Nitzschia, Ochromonas, Oedogonium, Oocystis, Ostreococcus, Parachlorella, Parietochloris, Pascheria, Pavlova, Pelagomonas, Plurodactylum, Phagus, Picochlorum, Platymonas, Pleurochrysis, Pleurococcus, Prototheca, Pseudochlorella, Pseudoneochloris, Pseudostaurastrum, Pyramimonas, Pyrobotrys, Scenedesmus, Schizochlamydella, Skeletonema, Spyrogyra, Stichococcus, Tetrachlorella, Tetraselmis, Thalassiosira, Tribonema, Vaucheria, Viridiella, Vischeria, and Volvox.
 3. The method of claim 1, wherein the mutant or recombinant microorganism is cultured in a medium that comprises less than about 2.5 mM ammonium.
 4. The method of claim 3, wherein the mutant or recombinant microorganism is cultured in a medium that comprises less than about 1 mM ammonium.
 5. The method of claim 1, wherein the culture medium comprises nitrate.
 6. The method of claim 5, wherein the culture medium comprises at least about 2 mM nitrate.
 7. The method of claim 6, wherein the culture medium comprises at least about 5 mM nitrate.
 8. The method of claim 1, wherein the culture medium comprises urea.
 9. The method of claim 8, wherein the culture medium comprises at least about 2 mM urea.
 10. The method of claim 9, wherein the culture medium comprises at least about 5 mM urea.
 11. The method of claim 1, comprising culturing a microorganism conditions in which the FAME to total organic carbon (TOC) ratio of the microorganism is maintained between 0.3 and 0.9, and isolating lipid from the microorganism, the culture medium, or both.
 12. A method according to claim 11, wherein the FAME to TOC ratio is between about 0.4 and about 0.8.
 13. A method according to claim 12, wherein the FAME to TOC ratio is between about 0.4 and about 0.7.
 14. A method according to claim 13, wherein the FAME to TOC ratio is between about 0.4 and about 0.6.
 15. A method according to claim 14, wherein the FAME to TOC ratio is between about 0.45 and about 0.55.
 16. A method of claim 1, wherein the mutant microorganism has attenuated expression of a gene encoding a polypeptide regulating lipid production.
 17. A method of claim 1 wherein the mutant algal or heterokont microorganism produces at least 50% more fatty acid methyl ester-derivatizable lipids (FAME lipids) than a control algal or heterokont microorganism and at least 70% of the amount of biomass produced by the control microorganism when the mutant microorganism and control microorganism are cultured under identical conditions. 